---
source: src/gnomad_nuclear/pbs.rs
expression: records
---
- chrom: "1"
  pos: 55505599
  ref_allele: C
  alt_allele: G
  filters: []
  vep:
    - allele: G
      consequence: missense_variant
      impact: MODERATE
      symbol: PCSK9
      gene: ENSG00000169174
      feature_type: Transcript
      feature: ENST00000302118
      feature_biotype: protein_coding
      exon: 1/12
      intron: ~
      hgvsc: "ENST00000302118.5:c.89C>G"
      hgvsp: "ENSP00000303208.5:p.Ala30Gly"
      cdna_position: "379"
      cds_position: "89"
      protein_position: "30"
      amino_acids: A/G
      codons: gCg/gGg
      existing_variation: ~
      dbsnp_id: "1"
      distance: ~
      strand: "1"
      flags: ~
      variant_class: SNV
      minimised: "1"
      symbol_source: HGNC
      hgnc_id: "20001"
      canonical: true
      tsl: ~
      appris: ~
      ccds: CCDS603.1
      ensp: ENSP00000303208
      swissprot: Q8NBP7
      trembl: ~
      uniparc: UPI00001615E1
      gene_pheno: "1"
      sift:
        prediction: deleterious_low_confidence
        score: 0.03
      polyphen:
        prediction: possibly_damaging
        score: 0.583
      domains:
        - id: SignalP-noTM
          source: Cleavage_site_(Signalp)
        - id: PTHR10795
          source: hmmpanther
        - id: PTHR10795
          source: hmmpanther
      hgvs_offset: ~
      gmaf: ~
      afr_maf: ~
      amr_maf: ~
      eas_maf: ~
      eur_maf: ~
      sas_maf: ~
      aa_maf: ~
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: ~
      exac_afr_maf: ~
      exac_amr_maf: ~
      exac_eas_maf: ~
      exac_fin_maf: ~
      exac_nfe_maf: ~
      exac_oth_maf: ~
      exac_sas_maf: ~
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: "DE_NOVO_DONOR_PROB:0.146539915246404&MUTANT_DONOR_MES:8.16693067332728&DE_NOVO_DONOR_POS:-119&INTRON_END:55509515&DE_NOVO_DONOR_MES_POS:-122&INTRON_START:55505718&EXON_END:55505717&EXON_START:55505221&DE_NOVO_DONOR_MES:-1.61109392005567"
    - allele: G
      consequence: missense_variant
      impact: MODERATE
      symbol: PCSK9
      gene: ENSG00000169174
      feature_type: Transcript
      feature: ENST00000452118
      feature_biotype: protein_coding
      exon: 1/6
      intron: ~
      hgvsc: "ENST00000452118.2:c.89C>G"
      hgvsp: "ENSP00000401598.2:p.Ala30Gly"
      cdna_position: "169"
      cds_position: "89"
      protein_position: "30"
      amino_acids: A/G
      codons: gCg/gGg
      existing_variation: ~
      dbsnp_id: "1"
      distance: ~
      strand: "1"
      flags: ~
      variant_class: SNV
      minimised: "1"
      symbol_source: HGNC
      hgnc_id: "20001"
      canonical: false
      tsl: ~
      appris: ~
      ccds: ~
      ensp: ENSP00000401598
      swissprot: ~
      trembl: B4DEZ9
      uniparc: UPI00017A6F55
      gene_pheno: "1"
      sift:
        prediction: deleterious_low_confidence
        score: 0.02
      polyphen:
        prediction: possibly_damaging
        score: 0.655
      domains:
        - id: SignalP-noTM
          source: Cleavage_site_(Signalp)
        - id: PTHR10795
          source: hmmpanther
      hgvs_offset: ~
      gmaf: ~
      afr_maf: ~
      amr_maf: ~
      eas_maf: ~
      eur_maf: ~
      sas_maf: ~
      aa_maf: ~
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: ~
      exac_afr_maf: ~
      exac_amr_maf: ~
      exac_eas_maf: ~
      exac_fin_maf: ~
      exac_nfe_maf: ~
      exac_oth_maf: ~
      exac_sas_maf: ~
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: "DE_NOVO_DONOR_MES_POS:-122&INTRON_START:55505718&INTRON_END:55509515&EXON_START:55505431&DE_NOVO_DONOR_MES:-1.61109392005567&EXON_END:55505717&MUTANT_DONOR_MES:8.16693067332728&DE_NOVO_DONOR_PROB:0.146539915246404&DE_NOVO_DONOR_POS:-119"
    - allele: G
      consequence: upstream_gene_variant
      impact: MODIFIER
      symbol: PCSK9
      gene: ENSG00000169174
      feature_type: Transcript
      feature: ENST00000543384
      feature_biotype: protein_coding
      exon: ~
      intron: ~
      hgvsc: ~
      hgvsp: ~
      cdna_position: ~
      cds_position: ~
      protein_position: ~
      amino_acids: ~
      codons: ~
      existing_variation: ~
      dbsnp_id: "1"
      distance: "296"
      strand: "1"
      flags: ~
      variant_class: SNV
      minimised: "1"
      symbol_source: HGNC
      hgnc_id: "20001"
      canonical: false
      tsl: ~
      appris: ~
      ccds: ~
      ensp: ENSP00000441859
      swissprot: ~
      trembl: F5GWF0
      uniparc: UPI000206501F
      gene_pheno: "1"
      sift: ~
      polyphen: ~
      domains: []
      hgvs_offset: ~
      gmaf: ~
      afr_maf: ~
      amr_maf: ~
      eas_maf: ~
      eur_maf: ~
      sas_maf: ~
      aa_maf: ~
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: ~
      exac_afr_maf: ~
      exac_amr_maf: ~
      exac_eas_maf: ~
      exac_fin_maf: ~
      exac_nfe_maf: ~
      exac_oth_maf: ~
      exac_sas_maf: ~
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: ~
    - allele: G
      consequence: regulatory_region_variant
      impact: MODIFIER
      symbol: ""
      gene: ""
      feature_type: RegulatoryFeature
      feature: ENSR00001037993
      feature_biotype: promoter
      exon: ~
      intron: ~
      hgvsc: ~
      hgvsp: ~
      cdna_position: ~
      cds_position: ~
      protein_position: ~
      amino_acids: ~
      codons: ~
      existing_variation: ~
      dbsnp_id: "1"
      distance: ~
      strand: ~
      flags: ~
      variant_class: SNV
      minimised: "1"
      symbol_source: ~
      hgnc_id: ~
      canonical: false
      tsl: ~
      appris: ~
      ccds: ~
      ensp: ~
      swissprot: ~
      trembl: ~
      uniparc: ~
      gene_pheno: ~
      sift: ~
      polyphen: ~
      domains: []
      hgvs_offset: ~
      gmaf: ~
      afr_maf: ~
      amr_maf: ~
      eas_maf: ~
      eur_maf: ~
      sas_maf: ~
      aa_maf: ~
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: ~
      exac_afr_maf: ~
      exac_amr_maf: ~
      exac_eas_maf: ~
      exac_fin_maf: ~
      exac_nfe_maf: ~
      exac_oth_maf: ~
      exac_sas_maf: ~
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: ~
  allele_counts:
    - cohort: ~
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 10278
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 6396
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 3882
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 26912
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 15498
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 11414
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 8820
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 4180
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4640
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 13152
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 6510
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 6642
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 16514
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 8530
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 7984
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 2
              an: 74572
              nhomalt: 0
              af: 0.0000268197
            female:
              ac: 1
              an: 33698
              nhomalt: 0
              af: 0.0000296754
            male:
              ac: 1
              an: 40874
              nhomalt: 0
              af: 0.0000244654
          faf95: 0.00000445
          faf99: 0.00000467
        - population: oth
          counts:
            overall:
              ac: 0
              an: 4864
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2342
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2522
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 0
              an: 24186
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 6130
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 18056
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
      by_sex:
        overall:
          ac: 2
          an: 179298
          nhomalt: 0
          af: 0.0000111546
        female:
          ac: 1
          an: 83284
          nhomalt: 0
          af: 0.0000120071
        male:
          ac: 1
          an: 96014
          nhomalt: 0
          af: 0.0000104151
      raw:
        ac: 2
        an: 250244
        nhomalt: 0
        af: 0.0000079922
      popmax: nfe
      af_popmax: 0.0000268197
      ac_popmax: 2
      an_popmax: 74572
      nhomalt_popmax: 0
    - cohort: controls
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 3706
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2086
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 1620
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 13388
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 7848
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 5540
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 1628
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 812
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 816
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 5546
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2836
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2710
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 11740
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 6008
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 5732
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 2
              an: 26960
              nhomalt: 0
              af: 0.000074184
            female:
              ac: 1
              an: 12126
              nhomalt: 0
              af: 0.0000824674
            male:
              ac: 1
              an: 14834
              nhomalt: 0
              af: 0.0000674127
          faf95: 0.00000445
          faf99: 0.00000467
        - population: oth
          counts:
            overall:
              ac: 0
              an: 1500
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 748
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 752
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 0
              an: 12070
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 3364
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 8706
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
      by_sex:
        overall:
          ac: 2
          an: 76538
          nhomalt: 0
          af: 0.0000261308
        female:
          ac: 1
          an: 35828
          nhomalt: 0
          af: 0.0000279111
        male:
          ac: 1
          an: 40710
          nhomalt: 0
          af: 0.000024564
      raw:
        ac: 2
        an: 108948
        nhomalt: 0
        af: 0.0000183574
      popmax: nfe
      af_popmax: 0.000074184
      ac_popmax: 2
      an_popmax: 26960
      nhomalt_popmax: 0
    - cohort: non_cancer
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 9588
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 5892
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 3696
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 26772
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 15412
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 11360
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 8582
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 4050
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4532
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 12820
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 6314
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 6506
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 16508
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 8526
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 7982
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 2
              an: 69892
              nhomalt: 0
              af: 0.0000286156
            female:
              ac: 1
              an: 30948
              nhomalt: 0
              af: 0.0000323123
            male:
              ac: 1
              an: 38944
              nhomalt: 0
              af: 0.0000256779
          faf95: 0.00000445
          faf99: 0.00000467
        - population: oth
          counts:
            overall:
              ac: 0
              an: 4670
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2236
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2434
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 0
              an: 24158
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 6112
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 18046
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
      by_sex:
        overall:
          ac: 2
          an: 172990
          nhomalt: 0
          af: 0.0000115614
        female:
          ac: 1
          an: 79490
          nhomalt: 0
          af: 0.0000125802
        male:
          ac: 1
          an: 93500
          nhomalt: 0
          af: 0.0000106952
      raw:
        ac: 2
        an: 236048
        nhomalt: 0
        af: 0.00000847285
      popmax: nfe
      af_popmax: 0.0000286156
      ac_popmax: 2
      an_popmax: 69892
      nhomalt_popmax: 0
    - cohort: non_neuro
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 10242
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 6380
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 3862
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 22850
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 13496
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 9354
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 5026
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2404
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2622
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 10236
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 5050
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 5186
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 13938
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 7000
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 6938
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 2
              an: 59746
              nhomalt: 0
              af: 0.000033475
            female:
              ac: 1
              an: 27742
              nhomalt: 0
              af: 0.0000360464
            male:
              ac: 1
              an: 32004
              nhomalt: 0
              af: 0.0000312461
          faf95: 0.00000445
          faf99: 0.00000467
        - population: oth
          counts:
            overall:
              ac: 0
              an: 3880
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 1920
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 1960
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 0
              an: 24180
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 6130
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 18050
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
      by_sex:
        overall:
          ac: 2
          an: 150098
          nhomalt: 0
          af: 0.0000133246
        female:
          ac: 1
          an: 70122
          nhomalt: 0
          af: 0.0000142609
        male:
          ac: 1
          an: 79976
          nhomalt: 0
          af: 0.0000125038
      raw:
        ac: 2
        an: 207100
        nhomalt: 0
        af: 0.00000965717
      popmax: nfe
      af_popmax: 0.000033475
      ac_popmax: 2
      an_popmax: 59746
      nhomalt_popmax: 0
    - cohort: non_topmed
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 9010
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 5548
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 3462
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 26844
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 15458
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 11386
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 8756
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 4144
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4612
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 13148
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 6510
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 6638
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 16512
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 8528
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 7984
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 2
              an: 72974
              nhomalt: 0
              af: 0.000027407
            female:
              ac: 1
              an: 32716
              nhomalt: 0
              af: 0.0000305661
            male:
              ac: 1
              an: 40258
              nhomalt: 0
              af: 0.0000248398
          faf95: 0.00000445
          faf99: 0.00000467
        - population: oth
          counts:
            overall:
              ac: 0
              an: 4798
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2302
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2496
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 0
              an: 24186
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 6130
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 18056
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
      by_sex:
        overall:
          ac: 2
          an: 176228
          nhomalt: 0
          af: 0.0000113489
        female:
          ac: 1
          an: 81336
          nhomalt: 0
          af: 0.0000122947
        male:
          ac: 1
          an: 94892
          nhomalt: 0
          af: 0.0000105383
      raw:
        ac: 2
        an: 243722
        nhomalt: 0
        af: 0.00000820607
      popmax: nfe
      af_popmax: 0.000027407
      ac_popmax: 2
      an_popmax: 72974
      nhomalt_popmax: 0
  nonpar: false
  rf_info:
    rf_tp_probability: 0.718866
    rf_positive_label: false
    rf_negative_label: false
    rf_label: ~
    rf_train: false
  variant_info:
    variant_type: snv
    allele_type: snv
    n_alt_alleles: 1
    was_mixed: false
    has_star: false
  quality_info:
    fs: 4.683
    inbreeding_coeff: -0.0078
    mq: 60
    mq_rank_sum: 0.099
    qd: 12.72
    read_pos_rank_sum: 0.198
    sor: 0.421
    vqsr_positive_train_site: false
    vqsr_negative_train_site: false
    base_q_rank_sum: -1.495
    clipping_rank_sum: -0.322
    dp: 9394121
    vqslod: 0.044
    vqsr_culprit: MQ
    segdup: false
    lcr: false
    decoy: false
    transmitted_singleton: false
    pab_max: 1
  age_info:
    age_hist_hom_bin_freq: []
    age_hist_hom_n_smaller: 0
    age_hist_hom_n_larger: 0
    age_hist_het_bin_freq: []
    age_hist_het_n_smaller: 0
    age_hist_het_n_larger: 0
  depth_info:
    dp_hist_all_n_larger: 13668
    dp_hist_alt_n_larger: 1
    dp_hist_all_bin_freq: []
    dp_hist_alt_bin_freq: []
- chrom: "1"
  pos: 55505615
  ref_allele: C
  alt_allele: T
  filters: []
  vep:
    - allele: T
      consequence: synonymous_variant
      impact: LOW
      symbol: PCSK9
      gene: ENSG00000169174
      feature_type: Transcript
      feature: ENST00000302118
      feature_biotype: protein_coding
      exon: 1/12
      intron: ~
      hgvsc: "ENST00000302118.5:c.105C>T"
      hgvsp: "ENST00000302118.5:c.105C>T(p.=)"
      cdna_position: "395"
      cds_position: "105"
      protein_position: "35"
      amino_acids: D
      codons: gaC/gaT
      existing_variation: rs533474523
      dbsnp_id: "1"
      distance: ~
      strand: "1"
      flags: ~
      variant_class: SNV
      minimised: "1"
      symbol_source: HGNC
      hgnc_id: "20001"
      canonical: true
      tsl: ~
      appris: ~
      ccds: CCDS603.1
      ensp: ENSP00000303208
      swissprot: Q8NBP7
      trembl: ~
      uniparc: UPI00001615E1
      gene_pheno: "1"
      sift: ~
      polyphen: ~
      domains:
        - id: PTHR10795
          source: hmmpanther
        - id: PTHR10795
          source: hmmpanther
      hgvs_offset: ~
      gmaf: 0.0002
      afr_maf: 0.0002414
      amr_maf: 0
      eas_maf: 0
      eur_maf: 0
      sas_maf: 0
      aa_maf: 0.001
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: 0
      exac_afr_maf: 0.00001679
      exac_amr_maf: 0
      exac_eas_maf: 0.00007421
      exac_fin_maf: 0
      exac_nfe_maf: 0
      exac_oth_maf: 0
      exac_sas_maf: 0
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: "DE_NOVO_DONOR_MES_POS:-106&INTRON_START:55505718&INTRON_END:55509515&EXON_START:55505221&DE_NOVO_DONOR_MES:-4.29805061924569&EXON_END:55505717&MUTANT_DONOR_MES:8.16693067332728&DE_NOVO_DONOR_PROB:0.0706215314144107&DE_NOVO_DONOR_POS:-105"
    - allele: T
      consequence: synonymous_variant
      impact: LOW
      symbol: PCSK9
      gene: ENSG00000169174
      feature_type: Transcript
      feature: ENST00000452118
      feature_biotype: protein_coding
      exon: 1/6
      intron: ~
      hgvsc: "ENST00000452118.2:c.105C>T"
      hgvsp: "ENST00000452118.2:c.105C>T(p.=)"
      cdna_position: "185"
      cds_position: "105"
      protein_position: "35"
      amino_acids: D
      codons: gaC/gaT
      existing_variation: rs533474523
      dbsnp_id: "1"
      distance: ~
      strand: "1"
      flags: ~
      variant_class: SNV
      minimised: "1"
      symbol_source: HGNC
      hgnc_id: "20001"
      canonical: false
      tsl: ~
      appris: ~
      ccds: ~
      ensp: ENSP00000401598
      swissprot: ~
      trembl: B4DEZ9
      uniparc: UPI00017A6F55
      gene_pheno: "1"
      sift: ~
      polyphen: ~
      domains:
        - id: PTHR10795
          source: hmmpanther
      hgvs_offset: ~
      gmaf: 0.0002
      afr_maf: 0.0002414
      amr_maf: 0
      eas_maf: 0
      eur_maf: 0
      sas_maf: 0
      aa_maf: 0.001
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: 0
      exac_afr_maf: 0.00001679
      exac_amr_maf: 0
      exac_eas_maf: 0.00007421
      exac_fin_maf: 0
      exac_nfe_maf: 0
      exac_oth_maf: 0
      exac_sas_maf: 0
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: "EXON_START:55505431&DE_NOVO_DONOR_MES:-4.29805061924569&EXON_END:55505717&DE_NOVO_DONOR_MES_POS:-106&INTRON_START:55505718&INTRON_END:55509515&DE_NOVO_DONOR_POS:-105&MUTANT_DONOR_MES:8.16693067332728&DE_NOVO_DONOR_PROB:0.0706215314144107"
    - allele: T
      consequence: upstream_gene_variant
      impact: MODIFIER
      symbol: PCSK9
      gene: ENSG00000169174
      feature_type: Transcript
      feature: ENST00000543384
      feature_biotype: protein_coding
      exon: ~
      intron: ~
      hgvsc: ~
      hgvsp: ~
      cdna_position: ~
      cds_position: ~
      protein_position: ~
      amino_acids: ~
      codons: ~
      existing_variation: rs533474523
      dbsnp_id: "1"
      distance: "280"
      strand: "1"
      flags: ~
      variant_class: SNV
      minimised: "1"
      symbol_source: HGNC
      hgnc_id: "20001"
      canonical: false
      tsl: ~
      appris: ~
      ccds: ~
      ensp: ENSP00000441859
      swissprot: ~
      trembl: F5GWF0
      uniparc: UPI000206501F
      gene_pheno: "1"
      sift: ~
      polyphen: ~
      domains: []
      hgvs_offset: ~
      gmaf: 0.0002
      afr_maf: 0.0002414
      amr_maf: 0
      eas_maf: 0
      eur_maf: 0
      sas_maf: 0
      aa_maf: 0.001
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: 0
      exac_afr_maf: 0.00001679
      exac_amr_maf: 0
      exac_eas_maf: 0.00007421
      exac_fin_maf: 0
      exac_nfe_maf: 0
      exac_oth_maf: 0
      exac_sas_maf: 0
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: ~
    - allele: T
      consequence: regulatory_region_variant
      impact: MODIFIER
      symbol: ""
      gene: ""
      feature_type: RegulatoryFeature
      feature: ENSR00001037993
      feature_biotype: promoter
      exon: ~
      intron: ~
      hgvsc: ~
      hgvsp: ~
      cdna_position: ~
      cds_position: ~
      protein_position: ~
      amino_acids: ~
      codons: ~
      existing_variation: rs533474523
      dbsnp_id: "1"
      distance: ~
      strand: ~
      flags: ~
      variant_class: SNV
      minimised: "1"
      symbol_source: ~
      hgnc_id: ~
      canonical: false
      tsl: ~
      appris: ~
      ccds: ~
      ensp: ~
      swissprot: ~
      trembl: ~
      uniparc: ~
      gene_pheno: ~
      sift: ~
      polyphen: ~
      domains: []
      hgvs_offset: ~
      gmaf: 0.0002
      afr_maf: 0.0002414
      amr_maf: 0
      eas_maf: 0
      eur_maf: 0
      sas_maf: 0
      aa_maf: 0.001
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: 0
      exac_afr_maf: 0.00001679
      exac_amr_maf: 0
      exac_eas_maf: 0.00007421
      exac_fin_maf: 0
      exac_nfe_maf: 0
      exac_oth_maf: 0
      exac_sas_maf: 0
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: ~
  allele_counts:
    - cohort: ~
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 10794
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 6732
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4062
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 27624
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 15906
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 11718
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 8924
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 4230
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4694
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 13610
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 6736
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 6874
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 16742
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 8614
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 8128
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 0
              an: 77906
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 35074
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 42832
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: oth
          counts:
            overall:
              ac: 0
              an: 4928
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2382
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2546
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 2
              an: 24344
              nhomalt: 0
              af: 0.0000821558
            female:
              ac: 1
              an: 6138
              nhomalt: 0
              af: 0.00016292
            male:
              ac: 1
              an: 18206
              nhomalt: 0
              af: 0.0000549269
          faf95: 0.00001459
          faf99: 0.00001408
      by_sex:
        overall:
          ac: 2
          an: 184872
          nhomalt: 0
          af: 0.0000108183
        female:
          ac: 1
          an: 85812
          nhomalt: 0
          af: 0.0000116534
        male:
          ac: 1
          an: 99060
          nhomalt: 0
          af: 0.0000100949
      raw:
        ac: 16
        an: 250468
        nhomalt: 0
        af: 0.0000638804
      popmax: sas
      af_popmax: 0.0000821558
      ac_popmax: 2
      an_popmax: 24344
      nhomalt_popmax: 0
    - cohort: controls
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 3926
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2244
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 1682
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 13816
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 8112
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 5704
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 1660
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 832
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 828
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 5850
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2986
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2864
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 11828
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 6044
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 5784
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 0
              an: 28324
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 12658
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 15666
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: oth
          counts:
            overall:
              ac: 0
              an: 1528
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 768
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 760
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 2
              an: 12162
              nhomalt: 0
              af: 0.000164447
            female:
              ac: 1
              an: 3368
              nhomalt: 0
              af: 0.000296912
            male:
              ac: 1
              an: 8794
              nhomalt: 0
              af: 0.000113714
          faf95: 0.00001459
          faf99: 0.00001408
      by_sex:
        overall:
          ac: 2
          an: 79094
          nhomalt: 0
          af: 0.0000252864
        female:
          ac: 1
          an: 37012
          nhomalt: 0
          af: 0.0000270183
        male:
          ac: 1
          an: 42082
          nhomalt: 0
          af: 0.0000237631
      raw:
        ac: 10
        an: 109012
        nhomalt: 0
        af: 0.000091733
      popmax: sas
      af_popmax: 0.000164447
      ac_popmax: 2
      an_popmax: 12162
      nhomalt_popmax: 0
    - cohort: non_cancer
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 10026
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 6204
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 3822
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 27472
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 15818
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 11654
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 8660
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 4086
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4574
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 13232
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 6522
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 6710
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 16734
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 8608
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 8126
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 0
              an: 72772
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 32110
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 40662
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: oth
          counts:
            overall:
              ac: 0
              an: 4708
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2260
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2448
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 2
              an: 24310
              nhomalt: 0
              af: 0.0000822707
            female:
              ac: 1
              an: 6120
              nhomalt: 0
              af: 0.000163399
            male:
              ac: 1
              an: 18190
              nhomalt: 0
              af: 0.0000549753
          faf95: 0.00001459
          faf99: 0.00001408
      by_sex:
        overall:
          ac: 2
          an: 177914
          nhomalt: 0
          af: 0.0000112414
        female:
          ac: 1
          an: 81728
          nhomalt: 0
          af: 0.0000122357
        male:
          ac: 1
          an: 96186
          nhomalt: 0
          af: 0.0000103965
      raw:
        ac: 14
        an: 236212
        nhomalt: 0
        af: 0.0000592688
      popmax: sas
      af_popmax: 0.0000822707
      ac_popmax: 2
      an_popmax: 24310
      nhomalt_popmax: 0
    - cohort: non_neuro
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 10758
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 6716
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4042
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 23562
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 13904
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 9658
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 5112
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2444
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2668
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 10492
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 5196
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 5296
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 14096
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 7048
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 7048
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 0
              an: 62434
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 28834
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 33600
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: oth
          counts:
            overall:
              ac: 0
              an: 3948
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 1964
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 1984
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 2
              an: 24338
              nhomalt: 0
              af: 0.000082176
            female:
              ac: 1
              an: 6138
              nhomalt: 0
              af: 0.00016292
            male:
              ac: 1
              an: 18200
              nhomalt: 0
              af: 0.0000549451
          faf95: 0.00001459
          faf99: 0.00001408
      by_sex:
        overall:
          ac: 2
          an: 154740
          nhomalt: 0
          af: 0.0000129249
        female:
          ac: 1
          an: 72244
          nhomalt: 0
          af: 0.000013842
        male:
          ac: 1
          an: 82496
          nhomalt: 0
          af: 0.0000121218
      raw:
        ac: 13
        an: 207276
        nhomalt: 0
        af: 0.0000627183
      popmax: sas
      af_popmax: 0.000082176
      ac_popmax: 2
      an_popmax: 24338
      nhomalt_popmax: 0
    - cohort: non_topmed
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 9346
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 5744
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 3602
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 27548
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 15860
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 11688
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 8850
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 4190
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4660
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 13606
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 6736
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 6870
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 16740
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 8612
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 8128
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 0
              an: 76176
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 33988
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 42188
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: oth
          counts:
            overall:
              ac: 0
              an: 4860
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2340
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2520
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 2
              an: 24344
              nhomalt: 0
              af: 0.0000821558
            female:
              ac: 1
              an: 6138
              nhomalt: 0
              af: 0.00016292
            male:
              ac: 1
              an: 18206
              nhomalt: 0
              af: 0.0000549269
          faf95: 0.00001459
          faf99: 0.00001408
      by_sex:
        overall:
          ac: 2
          an: 181470
          nhomalt: 0
          af: 0.0000110211
        female:
          ac: 1
          an: 83608
          nhomalt: 0
          af: 0.0000119606
        male:
          ac: 1
          an: 97862
          nhomalt: 0
          af: 0.0000102185
      raw:
        ac: 15
        an: 243924
        nhomalt: 0
        af: 0.0000614946
      popmax: sas
      af_popmax: 0.0000821558
      ac_popmax: 2
      an_popmax: 24344
      nhomalt_popmax: 0
  nonpar: false
  rf_info:
    rf_tp_probability: 0.160052
    rf_positive_label: false
    rf_negative_label: false
    rf_label: ~
    rf_train: false
  variant_info:
    variant_type: snv
    allele_type: snv
    n_alt_alleles: 1
    was_mixed: false
    has_star: false
  quality_info:
    fs: 0
    inbreeding_coeff: -0.0069
    mq: 60
    mq_rank_sum: -0.537
    qd: 8.06
    read_pos_rank_sum: -0.317
    sor: 0.655
    vqsr_positive_train_site: false
    vqsr_negative_train_site: false
    base_q_rank_sum: -1.589
    clipping_rank_sum: -0.572
    dp: 9465840
    vqslod: 0.1
    vqsr_culprit: MQ
    segdup: false
    lcr: false
    decoy: false
    transmitted_singleton: false
    pab_max: 1
  age_info:
    age_hist_hom_bin_freq: []
    age_hist_hom_n_smaller: 0
    age_hist_hom_n_larger: 0
    age_hist_het_bin_freq: []
    age_hist_het_n_smaller: 0
    age_hist_het_n_larger: 0
  depth_info:
    dp_hist_all_n_larger: 13666
    dp_hist_alt_n_larger: 1
    dp_hist_all_bin_freq: []
    dp_hist_alt_bin_freq: []
- chrom: "1"
  pos: 55516888
  ref_allele: G
  alt_allele: A
  filters: []
  vep:
    - allele: A
      consequence: intron_variant
      impact: MODIFIER
      symbol: PCSK9
      gene: ENSG00000169174
      feature_type: Transcript
      feature: ENST00000302118
      feature_biotype: protein_coding
      exon: ~
      intron: 3/11
      hgvsc: "ENST00000302118.5:c.524-1063G>A"
      hgvsp: ~
      cdna_position: ~
      cds_position: ~
      protein_position: ~
      amino_acids: ~
      codons: ~
      existing_variation: rs778104784
      dbsnp_id: "1"
      distance: ~
      strand: "1"
      flags: ~
      variant_class: SNV
      minimised: "1"
      symbol_source: HGNC
      hgnc_id: "20001"
      canonical: true
      tsl: ~
      appris: ~
      ccds: CCDS603.1
      ensp: ENSP00000303208
      swissprot: Q8NBP7
      trembl: ~
      uniparc: UPI00001615E1
      gene_pheno: "1"
      sift: ~
      polyphen: ~
      domains: []
      hgvs_offset: ~
      gmaf: ~
      afr_maf: ~
      amr_maf: ~
      eas_maf: ~
      eur_maf: ~
      sas_maf: ~
      aa_maf: ~
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: ~
      exac_afr_maf: ~
      exac_amr_maf: ~
      exac_eas_maf: ~
      exac_fin_maf: ~
      exac_nfe_maf: ~
      exac_oth_maf: ~
      exac_sas_maf: ~
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: ~
    - allele: A
      consequence: missense_variant
      impact: MODERATE
      symbol: PCSK9
      gene: ENSG00000169174
      feature_type: Transcript
      feature: ENST00000452118
      feature_biotype: protein_coding
      exon: 4/6
      intron: ~
      hgvsc: "ENST00000452118.2:c.547G>A"
      hgvsp: "ENSP00000401598.2:p.Gly183Ser"
      cdna_position: "627"
      cds_position: "547"
      protein_position: "183"
      amino_acids: G/S
      codons: Ggc/Agc
      existing_variation: rs778104784
      dbsnp_id: "1"
      distance: ~
      strand: "1"
      flags: ~
      variant_class: SNV
      minimised: "1"
      symbol_source: HGNC
      hgnc_id: "20001"
      canonical: false
      tsl: ~
      appris: ~
      ccds: ~
      ensp: ENSP00000401598
      swissprot: ~
      trembl: B4DEZ9
      uniparc: UPI00017A6F55
      gene_pheno: "1"
      sift:
        prediction: deleterious_low_confidence
        score: 0
      polyphen:
        prediction: possibly_damaging
        score: 0.86
      domains: []
      hgvs_offset: ~
      gmaf: ~
      afr_maf: ~
      amr_maf: ~
      eas_maf: ~
      eur_maf: ~
      sas_maf: ~
      aa_maf: ~
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: ~
      exac_afr_maf: ~
      exac_amr_maf: ~
      exac_eas_maf: ~
      exac_fin_maf: ~
      exac_nfe_maf: ~
      exac_oth_maf: ~
      exac_sas_maf: ~
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: ~
    - allele: A
      consequence: non_coding_transcript_exon_variant&non_coding_transcript_variant
      impact: MODIFIER
      symbol: PCSK9
      gene: ENSG00000169174
      feature_type: Transcript
      feature: ENST00000490692
      feature_biotype: processed_transcript
      exon: 1/8
      intron: ~
      hgvsc: "ENST00000490692.1:n.282G>A"
      hgvsp: ~
      cdna_position: "282"
      cds_position: ~
      protein_position: ~
      amino_acids: ~
      codons: ~
      existing_variation: rs778104784
      dbsnp_id: "1"
      distance: ~
      strand: "1"
      flags: ~
      variant_class: SNV
      minimised: "1"
      symbol_source: HGNC
      hgnc_id: "20001"
      canonical: false
      tsl: ~
      appris: ~
      ccds: ~
      ensp: ~
      swissprot: ~
      trembl: ~
      uniparc: ~
      gene_pheno: "1"
      sift: ~
      polyphen: ~
      domains: []
      hgvs_offset: ~
      gmaf: ~
      afr_maf: ~
      amr_maf: ~
      eas_maf: ~
      eur_maf: ~
      sas_maf: ~
      aa_maf: ~
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: ~
      exac_afr_maf: ~
      exac_amr_maf: ~
      exac_eas_maf: ~
      exac_fin_maf: ~
      exac_nfe_maf: ~
      exac_oth_maf: ~
      exac_sas_maf: ~
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: ~
    - allele: A
      consequence: intron_variant
      impact: MODIFIER
      symbol: PCSK9
      gene: ENSG00000169174
      feature_type: Transcript
      feature: ENST00000543384
      feature_biotype: protein_coding
      exon: ~
      intron: 1/9
      hgvsc: "ENST00000543384.1:c.-77-1063G>A"
      hgvsp: ~
      cdna_position: ~
      cds_position: ~
      protein_position: ~
      amino_acids: ~
      codons: ~
      existing_variation: rs778104784
      dbsnp_id: "1"
      distance: ~
      strand: "1"
      flags: ~
      variant_class: SNV
      minimised: "1"
      symbol_source: HGNC
      hgnc_id: "20001"
      canonical: false
      tsl: ~
      appris: ~
      ccds: ~
      ensp: ENSP00000441859
      swissprot: ~
      trembl: F5GWF0
      uniparc: UPI000206501F
      gene_pheno: "1"
      sift: ~
      polyphen: ~
      domains: []
      hgvs_offset: ~
      gmaf: ~
      afr_maf: ~
      amr_maf: ~
      eas_maf: ~
      eur_maf: ~
      sas_maf: ~
      aa_maf: ~
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: ~
      exac_afr_maf: ~
      exac_amr_maf: ~
      exac_eas_maf: ~
      exac_fin_maf: ~
      exac_nfe_maf: ~
      exac_oth_maf: ~
      exac_sas_maf: ~
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: ~
  allele_counts:
    - cohort: ~
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 6082
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 3486
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2596
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 24326
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 14030
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 10296
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 8088
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 3812
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4276
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 10426
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 5084
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 5342
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 5380
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2762
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2618
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 0
              an: 47556
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 21402
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 26154
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: oth
          counts:
            overall:
              ac: 0
              an: 3988
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 1924
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2064
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 8
              an: 22384
              nhomalt: 0
              af: 0.000357398
            female:
              ac: 3
              an: 5516
              nhomalt: 0
              af: 0.000543872
            male:
              ac: 5
              an: 16868
              nhomalt: 0
              af: 0.000296419
          faf95: 0.00017773
          faf99: 0.00017709
      by_sex:
        overall:
          ac: 8
          an: 128230
          nhomalt: 0
          af: 0.0000623879
        female:
          ac: 3
          an: 58016
          nhomalt: 0
          af: 0.0000517099
        male:
          ac: 5
          an: 70214
          nhomalt: 0
          af: 0.0000712109
      raw:
        ac: 10
        an: 142752
        nhomalt: 0
        af: 0.0000700516
      popmax: sas
      af_popmax: 0.000357398
      ac_popmax: 8
      an_popmax: 22384
      nhomalt_popmax: 0
    - cohort: controls
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 2368
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 1344
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 1024
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 12120
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 7112
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 5008
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 1454
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 710
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 744
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 3994
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2008
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 1986
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 1506
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 668
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 838
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 0
              an: 18962
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 8658
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 10304
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: oth
          counts:
            overall:
              ac: 0
              an: 1272
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 640
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 632
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 4
              an: 11062
              nhomalt: 0
              af: 0.000361598
            female:
              ac: 1
              an: 2994
              nhomalt: 0
              af: 0.000334001
            male:
              ac: 3
              an: 8068
              nhomalt: 0
              af: 0.000371839
          faf95: 0.00017773
          faf99: 0.00017709
      by_sex:
        overall:
          ac: 4
          an: 52738
          nhomalt: 0
          af: 0.0000758466
        female:
          ac: 1
          an: 24134
          nhomalt: 0
          af: 0.0000414353
        male:
          ac: 3
          an: 28604
          nhomalt: 0
          af: 0.00010488
      raw:
        ac: 4
        an: 57802
        nhomalt: 0
        af: 0.0000692018
      popmax: sas
      af_popmax: 0.000361598
      ac_popmax: 4
      an_popmax: 11062
      nhomalt_popmax: 0
    - cohort: non_cancer
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 6078
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 3486
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2592
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 24324
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 14030
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 10294
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 8086
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 3812
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4274
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 10420
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 5084
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 5336
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 5380
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2762
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2618
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 0
              an: 47510
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 21382
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 26128
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: oth
          counts:
            overall:
              ac: 0
              an: 3988
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 1924
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2064
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 8
              an: 22384
              nhomalt: 0
              af: 0.000357398
            female:
              ac: 3
              an: 5516
              nhomalt: 0
              af: 0.000543872
            male:
              ac: 5
              an: 16868
              nhomalt: 0
              af: 0.000296419
          faf95: 0.00017773
          faf99: 0.00017709
      by_sex:
        overall:
          ac: 8
          an: 128170
          nhomalt: 0
          af: 0.0000624171
        female:
          ac: 3
          an: 57996
          nhomalt: 0
          af: 0.0000517277
        male:
          ac: 5
          an: 70174
          nhomalt: 0
          af: 0.0000712515
      raw:
        ac: 9
        an: 139372
        nhomalt: 0
        af: 0.0000645754
      popmax: sas
      af_popmax: 0.000357398
      ac_popmax: 8
      an_popmax: 22384
      nhomalt_popmax: 0
    - cohort: non_neuro
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 6050
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 3474
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2576
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 20320
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 12050
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 8270
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 4460
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2092
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2368
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 7920
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 3824
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4096
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 3506
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 1604
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 1902
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 0
              an: 42406
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 19602
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 22804
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: oth
          counts:
            overall:
              ac: 0
              an: 3284
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 1628
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 1656
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 8
              an: 22382
              nhomalt: 0
              af: 0.00035743
            female:
              ac: 3
              an: 5516
              nhomalt: 0
              af: 0.000543872
            male:
              ac: 5
              an: 16866
              nhomalt: 0
              af: 0.000296454
          faf95: 0.00017773
          faf99: 0.00017709
      by_sex:
        overall:
          ac: 8
          an: 110328
          nhomalt: 0
          af: 0.0000725111
        female:
          ac: 3
          an: 49790
          nhomalt: 0
          af: 0.0000602531
        male:
          ac: 5
          an: 60538
          nhomalt: 0
          af: 0.0000825928
      raw:
        ac: 10
        an: 121616
        nhomalt: 0
        af: 0.000082226
      popmax: sas
      af_popmax: 0.00035743
      ac_popmax: 8
      an_popmax: 22382
      nhomalt_popmax: 0
    - cohort: non_topmed
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 5912
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 3372
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2540
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 24272
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 14000
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 10272
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 8048
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 3794
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4254
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 10422
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 5084
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 5338
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 5378
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2760
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2618
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 0
              an: 46514
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 20834
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 25680
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: oth
          counts:
            overall:
              ac: 0
              an: 3938
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 1898
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2040
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 8
              an: 22384
              nhomalt: 0
              af: 0.000357398
            female:
              ac: 3
              an: 5516
              nhomalt: 0
              af: 0.000543872
            male:
              ac: 5
              an: 16868
              nhomalt: 0
              af: 0.000296419
          faf95: 0.00017773
          faf99: 0.00017709
      by_sex:
        overall:
          ac: 8
          an: 126868
          nhomalt: 0
          af: 0.0000630577
        female:
          ac: 3
          an: 57258
          nhomalt: 0
          af: 0.0000523944
        male:
          ac: 5
          an: 69610
          nhomalt: 0
          af: 0.0000718288
      raw:
        ac: 10
        an: 140614
        nhomalt: 0
        af: 0.0000711167
      popmax: sas
      af_popmax: 0.000357398
      ac_popmax: 8
      an_popmax: 22384
      nhomalt_popmax: 0
  nonpar: false
  rf_info:
    rf_tp_probability: 0.832565
    rf_positive_label: true
    rf_negative_label: false
    rf_label: TP
    rf_train: true
  variant_info:
    variant_type: mixed
    allele_type: snv
    n_alt_alleles: 3
    was_mixed: true
    has_star: false
  quality_info:
    fs: 0.568
    inbreeding_coeff: 0.0346
    mq: 59.75
    mq_rank_sum: 0.459
    qd: 15.76
    read_pos_rank_sum: 0
    sor: 0.767
    vqsr_positive_train_site: true
    vqsr_negative_train_site: false
    base_q_rank_sum: 1.45
    clipping_rank_sum: 0.137
    dp: 3701481
    vqslod: 6.1
    vqsr_culprit: FS
    segdup: false
    lcr: false
    decoy: false
    transmitted_singleton: false
    pab_max: 1
  age_info:
    age_hist_hom_bin_freq: []
    age_hist_hom_n_smaller: 0
    age_hist_hom_n_larger: 0
    age_hist_het_bin_freq: []
    age_hist_het_n_smaller: 0
    age_hist_het_n_larger: 0
  depth_info:
    dp_hist_all_n_larger: 26
    dp_hist_alt_n_larger: 0
    dp_hist_all_bin_freq: []
    dp_hist_alt_bin_freq: []
- chrom: "1"
  pos: 55516888
  ref_allele: G
  alt_allele: GA
  filters: []
  vep:
    - allele: A
      consequence: intron_variant
      impact: MODIFIER
      symbol: PCSK9
      gene: ENSG00000169174
      feature_type: Transcript
      feature: ENST00000302118
      feature_biotype: protein_coding
      exon: ~
      intron: 3/11
      hgvsc: "ENST00000302118.5:c.524-1063_524-1062insA"
      hgvsp: ~
      cdna_position: ~
      cds_position: ~
      protein_position: ~
      amino_acids: ~
      codons: ~
      existing_variation: rs527413419
      dbsnp_id: "1"
      distance: ~
      strand: "1"
      flags: ~
      variant_class: insertion
      minimised: "1"
      symbol_source: HGNC
      hgnc_id: "20001"
      canonical: true
      tsl: ~
      appris: ~
      ccds: CCDS603.1
      ensp: ENSP00000303208
      swissprot: Q8NBP7
      trembl: ~
      uniparc: UPI00001615E1
      gene_pheno: "1"
      sift: ~
      polyphen: ~
      domains: []
      hgvs_offset: ~
      gmaf: 0.0032
      afr_maf: ~
      amr_maf: 0.0113
      eas_maf: 0.0014
      eur_maf: 0
      sas_maf: 0
      aa_maf: 0
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: ~
      exac_afr_maf: ~
      exac_amr_maf: ~
      exac_eas_maf: ~
      exac_fin_maf: ~
      exac_nfe_maf: ~
      exac_oth_maf: ~
      exac_sas_maf: ~
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: ~
    - allele: A
      consequence: frameshift_variant
      impact: HIGH
      symbol: PCSK9
      gene: ENSG00000169174
      feature_type: Transcript
      feature: ENST00000452118
      feature_biotype: protein_coding
      exon: 4/6
      intron: ~
      hgvsc: "ENST00000452118.2:c.547_548insA"
      hgvsp: "ENSP00000401598.2:p.Gly183GlufsTer23"
      cdna_position: 627-628
      cds_position: 547-548
      protein_position: "183"
      amino_acids: G/EX
      codons: ggc/gAgc
      existing_variation: rs527413419
      dbsnp_id: "1"
      distance: ~
      strand: "1"
      flags: ~
      variant_class: insertion
      minimised: "1"
      symbol_source: HGNC
      hgnc_id: "20001"
      canonical: false
      tsl: ~
      appris: ~
      ccds: ~
      ensp: ENSP00000401598
      swissprot: ~
      trembl: B4DEZ9
      uniparc: UPI00017A6F55
      gene_pheno: "1"
      sift: ~
      polyphen: ~
      domains: []
      hgvs_offset: ~
      gmaf: 0.0032
      afr_maf: ~
      amr_maf: 0.0113
      eas_maf: 0.0014
      eur_maf: 0
      sas_maf: 0
      aa_maf: 0
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: ~
      exac_afr_maf: ~
      exac_amr_maf: ~
      exac_eas_maf: ~
      exac_fin_maf: ~
      exac_nfe_maf: ~
      exac_oth_maf: ~
      exac_sas_maf: ~
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: HC
      lof_filter: ~
      lof_flags: ~
      lof_info: "GERP_DIST:364.1444&BP_DIST:304&PERCENTILE:0.885113268608414&DIST_FROM_LAST_EXON:210&50_BP_RULE:PASS&PHYLOCSF_TOO_SHORT"
    - allele: A
      consequence: non_coding_transcript_exon_variant&non_coding_transcript_variant
      impact: MODIFIER
      symbol: PCSK9
      gene: ENSG00000169174
      feature_type: Transcript
      feature: ENST00000490692
      feature_biotype: processed_transcript
      exon: 1/8
      intron: ~
      hgvsc: "ENST00000490692.1:n.282_283insA"
      hgvsp: ~
      cdna_position: 282-283
      cds_position: ~
      protein_position: ~
      amino_acids: ~
      codons: ~
      existing_variation: rs527413419
      dbsnp_id: "1"
      distance: ~
      strand: "1"
      flags: ~
      variant_class: insertion
      minimised: "1"
      symbol_source: HGNC
      hgnc_id: "20001"
      canonical: false
      tsl: ~
      appris: ~
      ccds: ~
      ensp: ~
      swissprot: ~
      trembl: ~
      uniparc: ~
      gene_pheno: "1"
      sift: ~
      polyphen: ~
      domains: []
      hgvs_offset: ~
      gmaf: 0.0032
      afr_maf: ~
      amr_maf: 0.0113
      eas_maf: 0.0014
      eur_maf: 0
      sas_maf: 0
      aa_maf: 0
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: ~
      exac_afr_maf: ~
      exac_amr_maf: ~
      exac_eas_maf: ~
      exac_fin_maf: ~
      exac_nfe_maf: ~
      exac_oth_maf: ~
      exac_sas_maf: ~
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: ~
    - allele: A
      consequence: intron_variant
      impact: MODIFIER
      symbol: PCSK9
      gene: ENSG00000169174
      feature_type: Transcript
      feature: ENST00000543384
      feature_biotype: protein_coding
      exon: ~
      intron: 1/9
      hgvsc: "ENST00000543384.1:c.-77-1063_-77-1062insA"
      hgvsp: ~
      cdna_position: ~
      cds_position: ~
      protein_position: ~
      amino_acids: ~
      codons: ~
      existing_variation: rs527413419
      dbsnp_id: "1"
      distance: ~
      strand: "1"
      flags: ~
      variant_class: insertion
      minimised: "1"
      symbol_source: HGNC
      hgnc_id: "20001"
      canonical: false
      tsl: ~
      appris: ~
      ccds: ~
      ensp: ENSP00000441859
      swissprot: ~
      trembl: F5GWF0
      uniparc: UPI000206501F
      gene_pheno: "1"
      sift: ~
      polyphen: ~
      domains: []
      hgvs_offset: ~
      gmaf: 0.0032
      afr_maf: ~
      amr_maf: 0.0113
      eas_maf: 0.0014
      eur_maf: 0
      sas_maf: 0
      aa_maf: 0
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: ~
      exac_afr_maf: ~
      exac_amr_maf: ~
      exac_eas_maf: ~
      exac_fin_maf: ~
      exac_nfe_maf: ~
      exac_oth_maf: ~
      exac_sas_maf: ~
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: ~
  allele_counts:
    - cohort: ~
      by_population:
        - population: afr
          counts:
            overall:
              ac: 97
              an: 6082
              nhomalt: 2
              af: 0.0159487
            female:
              ac: 66
              an: 3486
              nhomalt: 1
              af: 0.0189329
            male:
              ac: 31
              an: 2596
              nhomalt: 1
              af: 0.0119414
          faf95: 0.0133815
          faf99: 0.0133811
        - population: amr
          counts:
            overall:
              ac: 18
              an: 24326
              nhomalt: 0
              af: 0.000739949
            female:
              ac: 11
              an: 14030
              nhomalt: 0
              af: 0.000784034
            male:
              ac: 7
              an: 10296
              nhomalt: 0
              af: 0.000679876
          faf95: 0.0004775
          faf99: 0.00047812
        - population: asj
          counts:
            overall:
              ac: 0
              an: 8088
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 3812
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4276
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 10426
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 5084
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 5342
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 5380
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2762
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2618
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 4
              an: 47556
              nhomalt: 0
              af: 0.0000841114
            female:
              ac: 2
              an: 21402
              nhomalt: 0
              af: 0.0000934492
            male:
              ac: 2
              an: 26154
              nhomalt: 0
              af: 0.0000764701
          faf95: 0.00002861
          faf99: 0.00002821
        - population: oth
          counts:
            overall:
              ac: 2
              an: 3988
              nhomalt: 0
              af: 0.000501505
            female:
              ac: 1
              an: 1924
              nhomalt: 0
              af: 0.000519751
            male:
              ac: 1
              an: 2064
              nhomalt: 0
              af: 0.000484496
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 0
              an: 22384
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 5516
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 16868
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
      by_sex:
        overall:
          ac: 121
          an: 128230
          nhomalt: 2
          af: 0.000943617
        female:
          ac: 80
          an: 58016
          nhomalt: 1
          af: 0.00137893
        male:
          ac: 41
          an: 70214
          nhomalt: 1
          af: 0.000583929
      raw:
        ac: 125
        an: 142752
        nhomalt: 3
        af: 0.000875644
      popmax: afr
      af_popmax: 0.0159487
      ac_popmax: 97
      an_popmax: 6082
      nhomalt_popmax: 2
    - cohort: controls
      by_population:
        - population: afr
          counts:
            overall:
              ac: 50
              an: 2368
              nhomalt: 1
              af: 0.0211149
            female:
              ac: 31
              an: 1344
              nhomalt: 0
              af: 0.0230655
            male:
              ac: 19
              an: 1024
              nhomalt: 1
              af: 0.0185547
          faf95: 0.0133815
          faf99: 0.0133811
        - population: amr
          counts:
            overall:
              ac: 12
              an: 12120
              nhomalt: 0
              af: 0.000990099
            female:
              ac: 8
              an: 7112
              nhomalt: 0
              af: 0.00112486
            male:
              ac: 4
              an: 5008
              nhomalt: 0
              af: 0.000798722
          faf95: 0.0004775
          faf99: 0.00047812
        - population: asj
          counts:
            overall:
              ac: 0
              an: 1454
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 710
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 744
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 3994
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2008
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 1986
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 1506
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 668
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 838
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 18962
              nhomalt: 0
              af: 0.0000527371
            female:
              ac: 1
              an: 8658
              nhomalt: 0
              af: 0.0001155
            male:
              ac: 0
              an: 10304
              nhomalt: 0
              af: 0
          faf95: 0.00002861
          faf99: 0.00002821
        - population: oth
          counts:
            overall:
              ac: 0
              an: 1272
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 640
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 632
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 0
              an: 11062
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2994
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 8068
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
      by_sex:
        overall:
          ac: 63
          an: 52738
          nhomalt: 1
          af: 0.00119458
        female:
          ac: 40
          an: 24134
          nhomalt: 0
          af: 0.00165741
        male:
          ac: 23
          an: 28604
          nhomalt: 1
          af: 0.000804083
      raw:
        ac: 64
        an: 57802
        nhomalt: 1
        af: 0.00110723
      popmax: afr
      af_popmax: 0.0211149
      ac_popmax: 50
      an_popmax: 2368
      nhomalt_popmax: 1
    - cohort: non_cancer
      by_population:
        - population: afr
          counts:
            overall:
              ac: 97
              an: 6078
              nhomalt: 2
              af: 0.0159592
            female:
              ac: 66
              an: 3486
              nhomalt: 1
              af: 0.0189329
            male:
              ac: 31
              an: 2592
              nhomalt: 1
              af: 0.0119599
          faf95: 0.0133815
          faf99: 0.0133811
        - population: amr
          counts:
            overall:
              ac: 18
              an: 24324
              nhomalt: 0
              af: 0.00074001
            female:
              ac: 11
              an: 14030
              nhomalt: 0
              af: 0.000784034
            male:
              ac: 7
              an: 10294
              nhomalt: 0
              af: 0.000680008
          faf95: 0.0004775
          faf99: 0.00047812
        - population: asj
          counts:
            overall:
              ac: 0
              an: 8086
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 3812
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4274
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 10420
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 5084
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 5336
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 5380
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2762
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2618
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 4
              an: 47510
              nhomalt: 0
              af: 0.0000841928
            female:
              ac: 2
              an: 21382
              nhomalt: 0
              af: 0.0000935366
            male:
              ac: 2
              an: 26128
              nhomalt: 0
              af: 0.0000765462
          faf95: 0.00002861
          faf99: 0.00002821
        - population: oth
          counts:
            overall:
              ac: 2
              an: 3988
              nhomalt: 0
              af: 0.000501505
            female:
              ac: 1
              an: 1924
              nhomalt: 0
              af: 0.000519751
            male:
              ac: 1
              an: 2064
              nhomalt: 0
              af: 0.000484496
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 0
              an: 22384
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 5516
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 16868
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
      by_sex:
        overall:
          ac: 121
          an: 128170
          nhomalt: 2
          af: 0.000944059
        female:
          ac: 80
          an: 57996
          nhomalt: 1
          af: 0.00137941
        male:
          ac: 41
          an: 70174
          nhomalt: 1
          af: 0.000584262
      raw:
        ac: 123
        an: 139372
        nhomalt: 2
        af: 0.00088253
      popmax: afr
      af_popmax: 0.0159592
      ac_popmax: 97
      an_popmax: 6078
      nhomalt_popmax: 2
    - cohort: non_neuro
      by_population:
        - population: afr
          counts:
            overall:
              ac: 97
              an: 6050
              nhomalt: 2
              af: 0.0160331
            female:
              ac: 66
              an: 3474
              nhomalt: 1
              af: 0.0189983
            male:
              ac: 31
              an: 2576
              nhomalt: 1
              af: 0.0120342
          faf95: 0.0133815
          faf99: 0.0133811
        - population: amr
          counts:
            overall:
              ac: 13
              an: 20320
              nhomalt: 0
              af: 0.000639764
            female:
              ac: 8
              an: 12050
              nhomalt: 0
              af: 0.0006639
            male:
              ac: 5
              an: 8270
              nhomalt: 0
              af: 0.000604595
          faf95: 0.0004775
          faf99: 0.00047812
        - population: asj
          counts:
            overall:
              ac: 0
              an: 4460
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2092
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2368
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 7920
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 3824
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4096
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 3506
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 1604
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 1902
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 2
              an: 42406
              nhomalt: 0
              af: 0.0000471631
            female:
              ac: 1
              an: 19602
              nhomalt: 0
              af: 0.0000510152
            male:
              ac: 1
              an: 22804
              nhomalt: 0
              af: 0.000043852
          faf95: 0.00002861
          faf99: 0.00002821
        - population: oth
          counts:
            overall:
              ac: 2
              an: 3284
              nhomalt: 0
              af: 0.000609013
            female:
              ac: 1
              an: 1628
              nhomalt: 0
              af: 0.000614251
            male:
              ac: 1
              an: 1656
              nhomalt: 0
              af: 0.000603865
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 0
              an: 22382
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 5516
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 16866
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
      by_sex:
        overall:
          ac: 114
          an: 110328
          nhomalt: 2
          af: 0.00103328
        female:
          ac: 76
          an: 49790
          nhomalt: 1
          af: 0.00152641
        male:
          ac: 38
          an: 60538
          nhomalt: 1
          af: 0.000627705
      raw:
        ac: 118
        an: 121616
        nhomalt: 3
        af: 0.000970267
      popmax: afr
      af_popmax: 0.0160331
      ac_popmax: 97
      an_popmax: 6050
      nhomalt_popmax: 2
    - cohort: non_topmed
      by_population:
        - population: afr
          counts:
            overall:
              ac: 90
              an: 5912
              nhomalt: 2
              af: 0.0152233
            female:
              ac: 61
              an: 3372
              nhomalt: 1
              af: 0.0180902
            male:
              ac: 29
              an: 2540
              nhomalt: 1
              af: 0.0114173
          faf95: 0.0133815
          faf99: 0.0133811
        - population: amr
          counts:
            overall:
              ac: 18
              an: 24272
              nhomalt: 0
              af: 0.000741595
            female:
              ac: 11
              an: 14000
              nhomalt: 0
              af: 0.000785714
            male:
              ac: 7
              an: 10272
              nhomalt: 0
              af: 0.000681464
          faf95: 0.0004775
          faf99: 0.00047812
        - population: asj
          counts:
            overall:
              ac: 0
              an: 8048
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 3794
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4254
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 10422
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 5084
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 5338
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 5378
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2760
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2618
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 4
              an: 46514
              nhomalt: 0
              af: 0.0000859956
            female:
              ac: 2
              an: 20834
              nhomalt: 0
              af: 0.0000959969
            male:
              ac: 2
              an: 25680
              nhomalt: 0
              af: 0.0000778816
          faf95: 0.00002861
          faf99: 0.00002821
        - population: oth
          counts:
            overall:
              ac: 2
              an: 3938
              nhomalt: 0
              af: 0.000507872
            female:
              ac: 1
              an: 1898
              nhomalt: 0
              af: 0.00052687
            male:
              ac: 1
              an: 2040
              nhomalt: 0
              af: 0.000490196
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 0
              an: 22384
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 5516
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 16868
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
      by_sex:
        overall:
          ac: 114
          an: 126868
          nhomalt: 2
          af: 0.000898572
        female:
          ac: 75
          an: 57258
          nhomalt: 1
          af: 0.00130986
        male:
          ac: 39
          an: 69610
          nhomalt: 1
          af: 0.000560264
      raw:
        ac: 118
        an: 140614
        nhomalt: 3
        af: 0.000839177
      popmax: afr
      af_popmax: 0.0152233
      ac_popmax: 90
      an_popmax: 5912
      nhomalt_popmax: 2
  nonpar: false
  rf_info:
    rf_tp_probability: 0.831697
    rf_positive_label: true
    rf_negative_label: false
    rf_label: TP
    rf_train: true
  variant_info:
    variant_type: mixed
    allele_type: ins
    n_alt_alleles: 3
    was_mixed: true
    has_star: false
  quality_info:
    fs: 0.568
    inbreeding_coeff: 0.0346
    mq: 59.75
    mq_rank_sum: 0.459
    qd: 15.76
    read_pos_rank_sum: 0
    sor: 0.767
    vqsr_positive_train_site: true
    vqsr_negative_train_site: false
    base_q_rank_sum: 1.45
    clipping_rank_sum: 0.137
    dp: 3701481
    vqslod: 6.1
    vqsr_culprit: FS
    segdup: false
    lcr: false
    decoy: false
    transmitted_singleton: false
    pab_max: 1
  age_info:
    age_hist_hom_bin_freq: []
    age_hist_hom_n_smaller: 0
    age_hist_hom_n_larger: 0
    age_hist_het_bin_freq: []
    age_hist_het_n_smaller: 9
    age_hist_het_n_larger: 1
  depth_info:
    dp_hist_all_n_larger: 26
    dp_hist_alt_n_larger: 0
    dp_hist_all_bin_freq: []
    dp_hist_alt_bin_freq: []
- chrom: X
  pos: 69902557
  ref_allele: G
  alt_allele: T
  filters: []
  vep:
    - allele: T
      consequence: missense_variant
      impact: MODERATE
      symbol: TEX11
      gene: ENSG00000120498
      feature_type: Transcript
      feature: ENST00000344304
      feature_biotype: protein_coding
      exon: 13/29
      intron: ~
      hgvsc: "ENST00000344304.3:c.1168C>A"
      hgvsp: "ENSP00000340995.3:p.Leu390Ile"
      cdna_position: "1168"
      cds_position: "1168"
      protein_position: "390"
      amino_acids: L/I
      codons: Ctt/Att
      existing_variation: ~
      dbsnp_id: "1"
      distance: ~
      strand: "-1"
      flags: ~
      variant_class: SNV
      minimised: "1"
      symbol_source: HGNC
      hgnc_id: "11733"
      canonical: false
      tsl: ~
      appris: ~
      ccds: CCDS35323.1
      ensp: ENSP00000340995
      swissprot: Q8IYF3
      trembl: ~
      uniparc: UPI000013CA89
      gene_pheno: "1"
      sift:
        prediction: tolerated
        score: 0.17
      polyphen:
        prediction: benign
        score: 0.105
      domains:
        - id: seg
          source: Low_complexity_(Seg)
        - id: PTHR22904
          source: hmmpanther
        - id: PTHR22904
          source: hmmpanther
        - id: PF08631
          source: Pfam_domain
      hgvs_offset: ~
      gmaf: ~
      afr_maf: ~
      amr_maf: ~
      eas_maf: ~
      eur_maf: ~
      sas_maf: ~
      aa_maf: ~
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: ~
      exac_afr_maf: ~
      exac_amr_maf: ~
      exac_eas_maf: ~
      exac_fin_maf: ~
      exac_nfe_maf: ~
      exac_oth_maf: ~
      exac_sas_maf: ~
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: ~
    - allele: T
      consequence: missense_variant
      impact: MODERATE
      symbol: TEX11
      gene: ENSG00000120498
      feature_type: Transcript
      feature: ENST00000374320
      feature_biotype: protein_coding
      exon: 3/19
      intron: ~
      hgvsc: "ENST00000374320.2:c.193C>A"
      hgvsp: "ENSP00000363440.2:p.Leu65Ile"
      cdna_position: "415"
      cds_position: "193"
      protein_position: "65"
      amino_acids: L/I
      codons: Ctt/Att
      existing_variation: ~
      dbsnp_id: "1"
      distance: ~
      strand: "-1"
      flags: ~
      variant_class: SNV
      minimised: "1"
      symbol_source: HGNC
      hgnc_id: "11733"
      canonical: false
      tsl: ~
      appris: ~
      ccds: ~
      ensp: ENSP00000363440
      swissprot: Q8IYF3
      trembl: ~
      uniparc: UPI00004A2D6C
      gene_pheno: "1"
      sift:
        prediction: tolerated
        score: 0.12
      polyphen:
        prediction: benign
        score: 0.105
      domains:
        - id: seg
          source: Low_complexity_(Seg)
        - id: PTHR22904
          source: hmmpanther
        - id: PTHR22904
          source: hmmpanther
        - id: PF08631
          source: Pfam_domain
      hgvs_offset: ~
      gmaf: ~
      afr_maf: ~
      amr_maf: ~
      eas_maf: ~
      eur_maf: ~
      sas_maf: ~
      aa_maf: ~
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: ~
      exac_afr_maf: ~
      exac_amr_maf: ~
      exac_eas_maf: ~
      exac_fin_maf: ~
      exac_nfe_maf: ~
      exac_oth_maf: ~
      exac_sas_maf: ~
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: ~
    - allele: T
      consequence: missense_variant
      impact: MODERATE
      symbol: TEX11
      gene: ENSG00000120498
      feature_type: Transcript
      feature: ENST00000374333
      feature_biotype: protein_coding
      exon: 14/30
      intron: ~
      hgvsc: "ENST00000374333.2:c.1123C>A"
      hgvsp: "ENSP00000363453.2:p.Leu375Ile"
      cdna_position: "1222"
      cds_position: "1123"
      protein_position: "375"
      amino_acids: L/I
      codons: Ctt/Att
      existing_variation: ~
      dbsnp_id: "1"
      distance: ~
      strand: "-1"
      flags: ~
      variant_class: SNV
      minimised: "1"
      symbol_source: HGNC
      hgnc_id: "11733"
      canonical: false
      tsl: ~
      appris: ~
      ccds: CCDS43968.1
      ensp: ENSP00000363453
      swissprot: Q8IYF3
      trembl: ~
      uniparc: UPI00002122F2
      gene_pheno: "1"
      sift:
        prediction: tolerated
        score: 0.18
      polyphen:
        prediction: benign
        score: 0.416
      domains:
        - id: seg
          source: Low_complexity_(Seg)
        - id: PTHR22904
          source: hmmpanther
        - id: PTHR22904
          source: hmmpanther
        - id: PF08631
          source: Pfam_domain
      hgvs_offset: ~
      gmaf: ~
      afr_maf: ~
      amr_maf: ~
      eas_maf: ~
      eur_maf: ~
      sas_maf: ~
      aa_maf: ~
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: ~
      exac_afr_maf: ~
      exac_amr_maf: ~
      exac_eas_maf: ~
      exac_fin_maf: ~
      exac_nfe_maf: ~
      exac_oth_maf: ~
      exac_sas_maf: ~
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: ~
    - allele: T
      consequence: missense_variant
      impact: MODERATE
      symbol: TEX11
      gene: ENSG00000120498
      feature_type: Transcript
      feature: ENST00000395889
      feature_biotype: protein_coding
      exon: 15/31
      intron: ~
      hgvsc: "ENST00000395889.2:c.1168C>A"
      hgvsp: "ENSP00000379226.2:p.Leu390Ile"
      cdna_position: "1324"
      cds_position: "1168"
      protein_position: "390"
      amino_acids: L/I
      codons: Ctt/Att
      existing_variation: ~
      dbsnp_id: "1"
      distance: ~
      strand: "-1"
      flags: ~
      variant_class: SNV
      minimised: "1"
      symbol_source: HGNC
      hgnc_id: "11733"
      canonical: true
      tsl: ~
      appris: ~
      ccds: CCDS35323.1
      ensp: ENSP00000379226
      swissprot: Q8IYF3
      trembl: ~
      uniparc: UPI000013CA89
      gene_pheno: "1"
      sift:
        prediction: tolerated
        score: 0.17
      polyphen:
        prediction: benign
        score: 0.105
      domains:
        - id: seg
          source: Low_complexity_(Seg)
        - id: PTHR22904
          source: hmmpanther
        - id: PTHR22904
          source: hmmpanther
        - id: PF08631
          source: Pfam_domain
      hgvs_offset: ~
      gmaf: ~
      afr_maf: ~
      amr_maf: ~
      eas_maf: ~
      eur_maf: ~
      sas_maf: ~
      aa_maf: ~
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: ~
      exac_afr_maf: ~
      exac_amr_maf: ~
      exac_eas_maf: ~
      exac_fin_maf: ~
      exac_nfe_maf: ~
      exac_oth_maf: ~
      exac_sas_maf: ~
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: ~
  allele_counts:
    - cohort: ~
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 12985
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 10040
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2945
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 26680
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 20200
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 6480
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 7378
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 4894
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2484
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 13726
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 9328
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4398
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 15957
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 10372
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 5585
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 80706
              nhomalt: 0
              af: 0.0000123907
            female:
              ac: 1
              an: 50044
              nhomalt: 0
              af: 0.0000199824
            male:
              ac: 0
              an: 30662
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: oth
          counts:
            overall:
              ac: 0
              an: 4453
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2916
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 1537
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 0
              an: 17436
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 7500
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 9936
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
      by_sex:
        overall:
          ac: 1
          an: 179321
          nhomalt: 0
          af: 0.00000557659
        female:
          ac: 1
          an: 115294
          nhomalt: 0
          af: 0.00000867348
        male:
          ac: 0
          an: 64027
          nhomalt: 0
          af: 0
      raw:
        ac: 1
        an: 183512
        nhomalt: 0
        af: 0.00000544923
      popmax: nfe
      af_popmax: 0.0000123907
      ac_popmax: 1
      an_popmax: 80706
      nhomalt_popmax: 0
    - cohort: controls
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 5598
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 4228
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 1370
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 13284
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 10180
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 3104
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 1727
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 1212
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 515
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 6882
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 4788
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2094
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 9919
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 6474
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 3445
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 30573
              nhomalt: 0
              af: 0.0000327086
            female:
              ac: 1
              an: 19134
              nhomalt: 0
              af: 0.000052263
            male:
              ac: 0
              an: 11439
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: oth
          counts:
            overall:
              ac: 0
              an: 1425
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 986
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 439
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 0
              an: 9216
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 4190
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 5026
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
      by_sex:
        overall:
          ac: 1
          an: 78624
          nhomalt: 0
          af: 0.0000127188
        female:
          ac: 1
          an: 51192
          nhomalt: 0
          af: 0.0000195343
        male:
          ac: 0
          an: 27432
          nhomalt: 0
          af: 0
      raw:
        ac: 1
        an: 80343
        nhomalt: 0
        af: 0.0000124466
      popmax: nfe
      af_popmax: 0.0000327086
      ac_popmax: 1
      an_popmax: 30573
      nhomalt_popmax: 0
    - cohort: non_cancer
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 11895
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 9202
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2693
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 26428
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 20016
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 6412
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 6978
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 4592
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2386
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 13196
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 8948
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4248
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 15943
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 10360
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 5583
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 72394
              nhomalt: 0
              af: 0.0000138133
            female:
              ac: 1
              an: 44222
              nhomalt: 0
              af: 0.0000226132
            male:
              ac: 0
              an: 28172
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: oth
          counts:
            overall:
              ac: 0
              an: 4076
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2674
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 1402
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 0
              an: 17367
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 7450
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 9917
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
      by_sex:
        overall:
          ac: 1
          an: 168277
          nhomalt: 0
          af: 0.00000594258
        female:
          ac: 1
          an: 107464
          nhomalt: 0
          af: 0.00000930544
        male:
          ac: 0
          an: 60813
          nhomalt: 0
          af: 0
      raw:
        ac: 1
        an: 172308
        nhomalt: 0
        af: 0.00000580356
      popmax: nfe
      af_popmax: 0.0000138133
      ac_popmax: 1
      an_popmax: 72394
      nhomalt_popmax: 0
    - cohort: non_neuro
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 12958
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 10024
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2934
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 23674
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 18198
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 5476
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 4590
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 3082
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 1508
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 10075
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 6842
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 3233
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 12165
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 7650
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4515
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 63622
              nhomalt: 0
              af: 0.0000157178
            female:
              ac: 1
              an: 39734
              nhomalt: 0
              af: 0.0000251674
            male:
              ac: 0
              an: 23888
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: oth
          counts:
            overall:
              ac: 0
              an: 3561
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2380
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 1181
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 0
              an: 17431
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 7498
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 9933
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
      by_sex:
        overall:
          ac: 1
          an: 148076
          nhomalt: 0
          af: 0.00000675329
        female:
          ac: 1
          an: 95408
          nhomalt: 0
          af: 0.0000104813
        male:
          ac: 0
          an: 52668
          nhomalt: 0
          af: 0
      raw:
        ac: 1
        an: 151877
        nhomalt: 0
        af: 0.00000658428
      popmax: nfe
      af_popmax: 0.0000157178
      ac_popmax: 1
      an_popmax: 63622
      nhomalt_popmax: 0
    - cohort: non_topmed
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 9592
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 7318
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2274
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 26580
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 20124
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 6456
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 7314
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 4848
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2466
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 13724
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 9328
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4396
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 15955
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 10370
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 5585
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 79001
              nhomalt: 0
              af: 0.0000126581
            female:
              ac: 1
              an: 48698
              nhomalt: 0
              af: 0.0000205347
            male:
              ac: 0
              an: 30303
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: oth
          counts:
            overall:
              ac: 0
              an: 4390
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 2866
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 1524
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 0
              an: 17436
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 7500
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 9936
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
      by_sex:
        overall:
          ac: 1
          an: 173992
          nhomalt: 0
          af: 0.00000574739
        female:
          ac: 1
          an: 111052
          nhomalt: 0
          af: 0.00000900479
        male:
          ac: 0
          an: 62940
          nhomalt: 0
          af: 0
      raw:
        ac: 1
        an: 178078
        nhomalt: 0
        af: 0.00000561552
      popmax: nfe
      af_popmax: 0.0000126581
      ac_popmax: 1
      an_popmax: 79001
      nhomalt_popmax: 0
  nonpar: true
  rf_info:
    rf_tp_probability: 0.706202
    rf_positive_label: false
    rf_negative_label: false
    rf_label: ~
    rf_train: false
  variant_info:
    variant_type: snv
    allele_type: snv
    n_alt_alleles: 1
    was_mixed: false
    has_star: false
  quality_info:
    fs: 0
    inbreeding_coeff: -0.0005
    mq: 59.25
    mq_rank_sum: 0.735
    qd: 10.72
    read_pos_rank_sum: 0.074
    sor: 0.652
    vqsr_positive_train_site: false
    vqsr_negative_train_site: false
    base_q_rank_sum: -4.839
    clipping_rank_sum: 0.149
    dp: 5945336
    vqslod: 1.16
    vqsr_culprit: MQ
    segdup: false
    lcr: false
    decoy: false
    transmitted_singleton: false
    pab_max: 0.264893
  age_info:
    age_hist_hom_bin_freq: []
    age_hist_hom_n_smaller: 0
    age_hist_hom_n_larger: 0
    age_hist_het_bin_freq: []
    age_hist_het_n_smaller: 0
    age_hist_het_n_larger: 1
  depth_info:
    dp_hist_all_n_larger: 509
    dp_hist_alt_n_larger: 1
    dp_hist_all_bin_freq: []
    dp_hist_alt_bin_freq: []
- chrom: Y
  pos: 4967199
  ref_allele: G
  alt_allele: T
  filters: []
  vep:
    - allele: T
      consequence: missense_variant
      impact: MODERATE
      symbol: PCDH11Y
      gene: ENSG00000099715
      feature_type: Transcript
      feature: ENST00000215473
      feature_biotype: protein_coding
      exon: 2/6
      intron: ~
      hgvsc: "ENST00000215473.6:c.1580G>T"
      hgvsp: "ENSP00000215473.6:p.Ser527Ile"
      cdna_position: "1580"
      cds_position: "1580"
      protein_position: "527"
      amino_acids: S/I
      codons: aGt/aTt
      existing_variation: ~
      dbsnp_id: "1"
      distance: ~
      strand: "1"
      flags: ~
      variant_class: SNV
      minimised: "1"
      symbol_source: HGNC
      hgnc_id: "15813"
      canonical: false
      tsl: ~
      appris: ~
      ccds: ~
      ensp: ENSP00000215473
      swissprot: ~
      trembl: Q70LR5&Q70LR4&J3QSR5
      uniparc: UPI0000D613B5
      gene_pheno: ~
      sift:
        prediction: deleterious
        score: 0
      polyphen:
        prediction: possibly_damaging
        score: 0.462
      domains:
        - id: PS50268
          source: PROSITE_profiles
        - id: PTHR24027
          source: hmmpanther
        - id: PTHR24027
          source: hmmpanther
        - id: 2.60.40.60
          source: Gene3D
        - id: PF00028
          source: Pfam_domain
        - id: SM00112
          source: SMART_domains
        - id: SSF49313
          source: Superfamily_domains
        - id: PR00205
          source: Prints_domain
      hgvs_offset: ~
      gmaf: ~
      afr_maf: ~
      amr_maf: ~
      eas_maf: ~
      eur_maf: ~
      sas_maf: ~
      aa_maf: ~
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: ~
      exac_afr_maf: ~
      exac_amr_maf: ~
      exac_eas_maf: ~
      exac_fin_maf: ~
      exac_nfe_maf: ~
      exac_oth_maf: ~
      exac_sas_maf: ~
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: ~
    - allele: T
      consequence: missense_variant
      impact: MODERATE
      symbol: PCDH11Y
      gene: ENSG00000099715
      feature_type: Transcript
      feature: ENST00000333703
      feature_biotype: protein_coding
      exon: 5/6
      intron: ~
      hgvsc: "ENST00000333703.4:c.1547G>T"
      hgvsp: "ENSP00000330552.4:p.Ser516Ile"
      cdna_position: "2060"
      cds_position: "1547"
      protein_position: "516"
      amino_acids: S/I
      codons: aGt/aTt
      existing_variation: ~
      dbsnp_id: "1"
      distance: ~
      strand: "1"
      flags: ~
      variant_class: SNV
      minimised: "1"
      symbol_source: HGNC
      hgnc_id: "15813"
      canonical: false
      tsl: ~
      appris: ~
      ccds: CCDS14776.1
      ensp: ENSP00000330552
      swissprot: Q9BZA8
      trembl: ~
      uniparc: UPI000006E1F2
      gene_pheno: ~
      sift:
        prediction: deleterious
        score: 0
      polyphen:
        prediction: possibly_damaging
        score: 0.517
      domains:
        - id: PS50268
          source: PROSITE_profiles
        - id: PTHR24027
          source: hmmpanther
        - id: PTHR24027
          source: hmmpanther
        - id: 2.60.40.60
          source: Gene3D
        - id: PF00028
          source: Pfam_domain
        - id: SM00112
          source: SMART_domains
        - id: SSF49313
          source: Superfamily_domains
        - id: PR00205
          source: Prints_domain
      hgvs_offset: ~
      gmaf: ~
      afr_maf: ~
      amr_maf: ~
      eas_maf: ~
      eur_maf: ~
      sas_maf: ~
      aa_maf: ~
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: ~
      exac_afr_maf: ~
      exac_amr_maf: ~
      exac_eas_maf: ~
      exac_fin_maf: ~
      exac_nfe_maf: ~
      exac_oth_maf: ~
      exac_sas_maf: ~
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: ~
    - allele: T
      consequence: missense_variant
      impact: MODERATE
      symbol: PCDH11Y
      gene: ENSG00000099715
      feature_type: Transcript
      feature: ENST00000362095
      feature_biotype: protein_coding
      exon: 2/3
      intron: ~
      hgvsc: "ENST00000362095.5:c.1580G>T"
      hgvsp: "ENSP00000355419.5:p.Ser527Ile"
      cdna_position: "2314"
      cds_position: "1580"
      protein_position: "527"
      amino_acids: S/I
      codons: aGt/aTt
      existing_variation: ~
      dbsnp_id: "1"
      distance: ~
      strand: "1"
      flags: ~
      variant_class: SNV
      minimised: "1"
      symbol_source: HGNC
      hgnc_id: "15813"
      canonical: true
      tsl: ~
      appris: ~
      ccds: CCDS14777.1
      ensp: ENSP00000355419
      swissprot: Q9BZA8
      trembl: ~
      uniparc: UPI000006EF4D
      gene_pheno: ~
      sift:
        prediction: deleterious
        score: 0
      polyphen:
        prediction: possibly_damaging
        score: 0.517
      domains:
        - id: PS50268
          source: PROSITE_profiles
        - id: PTHR24027
          source: hmmpanther
        - id: PTHR24027
          source: hmmpanther
        - id: PF00028
          source: Pfam_domain
        - id: 2.60.40.60
          source: Gene3D
        - id: SM00112
          source: SMART_domains
        - id: SSF49313
          source: Superfamily_domains
        - id: PR00205
          source: Prints_domain
      hgvs_offset: ~
      gmaf: ~
      afr_maf: ~
      amr_maf: ~
      eas_maf: ~
      eur_maf: ~
      sas_maf: ~
      aa_maf: ~
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: ~
      exac_afr_maf: ~
      exac_amr_maf: ~
      exac_eas_maf: ~
      exac_fin_maf: ~
      exac_nfe_maf: ~
      exac_oth_maf: ~
      exac_sas_maf: ~
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: ~
    - allele: T
      consequence: missense_variant
      impact: MODERATE
      symbol: PCDH11Y
      gene: ENSG00000099715
      feature_type: Transcript
      feature: ENST00000400457
      feature_biotype: protein_coding
      exon: 2/5
      intron: ~
      hgvsc: "ENST00000400457.2:c.1515G>T"
      hgvsp: "ENSP00000383306.2:p.Ser506Ile"
      cdna_position: "1515"
      cds_position: "1517"
      protein_position: "506"
      amino_acids: S/I
      codons: aGt/aTt
      existing_variation: ~
      dbsnp_id: "1"
      distance: ~
      strand: "1"
      flags: cds_start_NF
      variant_class: SNV
      minimised: "1"
      symbol_source: HGNC
      hgnc_id: "15813"
      canonical: false
      tsl: ~
      appris: ~
      ccds: ~
      ensp: ENSP00000383306
      swissprot: ~
      trembl: Q70LR5&Q70LR4
      uniparc: UPI000059DC01
      gene_pheno: ~
      sift:
        prediction: deleterious
        score: 0
      polyphen:
        prediction: possibly_damaging
        score: 0.517
      domains:
        - id: PS50268
          source: PROSITE_profiles
        - id: PTHR24027
          source: hmmpanther
        - id: PTHR24027
          source: hmmpanther
        - id: 2.60.40.60
          source: Gene3D
        - id: PF00028
          source: Pfam_domain
        - id: SM00112
          source: SMART_domains
        - id: SSF49313
          source: Superfamily_domains
        - id: PR00205
          source: Prints_domain
      hgvs_offset: ~
      gmaf: ~
      afr_maf: ~
      amr_maf: ~
      eas_maf: ~
      eur_maf: ~
      sas_maf: ~
      aa_maf: ~
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: ~
      exac_afr_maf: ~
      exac_amr_maf: ~
      exac_eas_maf: ~
      exac_fin_maf: ~
      exac_nfe_maf: ~
      exac_oth_maf: ~
      exac_sas_maf: ~
      clin_sig: ~
      somatic: ~
      pheno: ~
      pubmed: ~
      motif_name: ~
      motif_pos: ~
      high_inf_pos: ~
      motif_score_change: ~
      lof: ~
      lof_filter: ~
      lof_flags: ~
      lof_info: ~
  allele_counts:
    - cohort: ~
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 3092
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 3092
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 7157
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 7157
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 2587
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2587
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 4528
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4528
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 5636
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 5636
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 31633
              nhomalt: 0
              af: 0.0000316126
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 1
              an: 31633
              nhomalt: 0
              af: 0.0000316126
          faf95: 0
          faf99: 0
        - population: oth
          counts:
            overall:
              ac: 0
              an: 1603
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 1603
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 0
              an: 11530
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 11530
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
      by_sex:
        overall:
          ac: 1
          an: 67766
          nhomalt: 0
          af: 0.0000147567
        female:
          ac: 0
          an: 0
          nhomalt: 0
          af: 0
        male:
          ac: 1
          an: 67766
          nhomalt: 0
          af: 0.0000147567
      raw:
        ac: 1
        an: 67873
        nhomalt: 0
        af: 0.0000147334
      popmax: nfe
      af_popmax: 0.0000316126
      ac_popmax: 1
      an_popmax: 31633
      nhomalt_popmax: 0
    - cohort: controls
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 1461
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 1461
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 3441
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 3441
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 552
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 552
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 2128
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2128
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 3459
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 3459
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 0
              an: 11784
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 11784
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: oth
          counts:
            overall:
              ac: 0
              an: 463
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 463
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 0
              an: 5736
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 5736
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
      by_sex:
        overall:
          ac: 0
          an: 29024
          nhomalt: 0
          af: 0
        female:
          ac: 0
          an: 0
          nhomalt: 0
          af: 0
        male:
          ac: 0
          an: 29024
          nhomalt: 0
          af: 0
      raw:
        ac: 0
        an: 29057
        nhomalt: 0
        af: 0
      popmax: ~
      af_popmax: ~
      ac_popmax: ~
      an_popmax: ~
      nhomalt_popmax: ~
    - cohort: non_cancer
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 2835
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2835
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 7083
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 7083
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 2485
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2485
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 4367
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4367
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 5634
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 5634
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 29070
              nhomalt: 0
              af: 0.0000343997
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 1
              an: 29070
              nhomalt: 0
              af: 0.0000343997
          faf95: 0
          faf99: 0
        - population: oth
          counts:
            overall:
              ac: 0
              an: 1467
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 1467
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 0
              an: 11510
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 11510
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
      by_sex:
        overall:
          ac: 1
          an: 64451
          nhomalt: 0
          af: 0.0000155157
        female:
          ac: 0
          an: 0
          nhomalt: 0
          af: 0
        male:
          ac: 1
          an: 64451
          nhomalt: 0
          af: 0.0000155157
      raw:
        ac: 1
        an: 64542
        nhomalt: 0
        af: 0.0000154938
      popmax: nfe
      af_popmax: 0.0000343997
      ac_popmax: 1
      an_popmax: 29070
      nhomalt_popmax: 0
    - cohort: non_neuro
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 3081
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 3081
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 6125
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 6125
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 1561
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 1561
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 3286
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 3286
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 4541
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4541
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 24813
              nhomalt: 0
              af: 0.0000403015
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 1
              an: 24813
              nhomalt: 0
              af: 0.0000403015
          faf95: 0
          faf99: 0
        - population: oth
          counts:
            overall:
              ac: 0
              an: 1235
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 1235
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 0
              an: 11527
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 11527
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
      by_sex:
        overall:
          ac: 1
          an: 56169
          nhomalt: 0
          af: 0.0000178034
        female:
          ac: 0
          an: 0
          nhomalt: 0
          af: 0
        male:
          ac: 1
          an: 56169
          nhomalt: 0
          af: 0.0000178034
      raw:
        ac: 1
        an: 56230
        nhomalt: 0
        af: 0.0000177841
      popmax: nfe
      af_popmax: 0.0000403015
      ac_popmax: 1
      an_popmax: 24813
      nhomalt_popmax: 0
    - cohort: non_topmed
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 2342
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2342
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 7128
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 7128
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 2569
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 2569
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 4526
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 4526
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: fin
          counts:
            overall:
              ac: 0
              an: 5636
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 5636
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 31262
              nhomalt: 0
              af: 0.0000319877
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 1
              an: 31262
              nhomalt: 0
              af: 0.0000319877
          faf95: 0
          faf99: 0
        - population: oth
          counts:
            overall:
              ac: 0
              an: 1590
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 1590
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall:
              ac: 0
              an: 11530
              nhomalt: 0
              af: 0
            female:
              ac: 0
              an: 0
              nhomalt: 0
              af: 0
            male:
              ac: 0
              an: 11530
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
      by_sex:
        overall:
          ac: 1
          an: 66583
          nhomalt: 0
          af: 0.0000150188
        female:
          ac: 0
          an: 0
          nhomalt: 0
          af: 0
        male:
          ac: 1
          an: 66583
          nhomalt: 0
          af: 0.0000150188
      raw:
        ac: 1
        an: 66690
        nhomalt: 0
        af: 0.0000149948
      popmax: nfe
      af_popmax: 0.0000319877
      ac_popmax: 1
      an_popmax: 31262
      nhomalt_popmax: 0
  nonpar: true
  rf_info:
    rf_tp_probability: 0.779496
    rf_positive_label: false
    rf_negative_label: false
    rf_label: ~
    rf_train: false
  variant_info:
    variant_type: snv
    allele_type: snv
    n_alt_alleles: 1
    was_mixed: false
    has_star: false
  quality_info:
    fs: 0
    inbreeding_coeff: -0.0015
    mq: 54.15
    mq_rank_sum: ~
    qd: 32.98
    read_pos_rank_sum: ~
    sor: 1.091
    vqsr_positive_train_site: false
    vqsr_negative_train_site: true
    base_q_rank_sum: ~
    clipping_rank_sum: ~
    dp: 3965717
    vqslod: 3.32
    vqsr_culprit: MQ
    segdup: true
    lcr: false
    decoy: false
    transmitted_singleton: false
    pab_max: ~
  age_info:
    age_hist_hom_bin_freq: []
    age_hist_hom_n_smaller: 0
    age_hist_hom_n_larger: 0
    age_hist_het_bin_freq: []
    age_hist_het_n_smaller: 0
    age_hist_het_n_larger: 0
  depth_info:
    dp_hist_all_n_larger: 3
    dp_hist_alt_n_larger: 1
    dp_hist_all_bin_freq: []
    dp_hist_alt_bin_freq: []

