---
source: src/gnomad_pbs/gnomad2.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: "MUTANT_DONOR_MES:8.16693067332728&DE_NOVO_DONOR_MES:-1.61109392005567&DE_NOVO_DONOR_MES_POS:-122&EXON_END:55505717&INTRON_START:55505718&DE_NOVO_DONOR_PROB:0.146539915246404&INTRON_END:55509515&DE_NOVO_DONOR_POS:-119&EXON_START:55505221"
    - 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&DE_NOVO_DONOR_MES:-1.61109392005567&MUTANT_DONOR_MES:8.16693067332728&INTRON_END:55509515&DE_NOVO_DONOR_POS:-119&EXON_END:55505717&DE_NOVO_DONOR_PROB:0.146539915246404&INTRON_START:55505718&EXON_START:55505431"
    - 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: 8706
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 3678
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 5028
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 848
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 414
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 434
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 290
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 80
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 210
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 1558
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 538
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 1020
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_oea
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_kor
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: fin
          counts:
            overall:
              ac: 0
              an: 3476
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 1846
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 1630
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 15428
              nhomalt: 0
              af: 0.0000648172
            xx:
              ac: 1
              an: 6806
              nhomalt: 0
              af: 0.000146929
            xy:
              ac: 0
              an: 8622
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_est
          counts:
            overall:
              ac: 0
              an: 4592
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_nwe
          counts:
            overall:
              ac: 0
              an: 8594
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_onf
          counts:
            overall:
              ac: 0
              an: 2136
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_seu
          counts:
            overall:
              ac: 1
              an: 106
              nhomalt: 0
              af: 0.00943396
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_swe
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: oth
          counts:
            overall:
              ac: 0
              an: 1086
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 560
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 526
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
      by_sex:
        overall:
          ac: 1
          an: 31392
          nhomalt: 0
          af: 0.0000318552
        xx:
          ac: 1
          an: 13922
          nhomalt: 0
          af: 0.0000718288
        xy:
          ac: 0
          an: 17470
          nhomalt: 0
          af: 0
      raw:
        ac: 1
        an: 31416
        nhomalt: 0
        af: 0.0000318309
      popmax: nfe
      af_popmax: 0.0000648172
      ac_popmax: 1
      an_popmax: 15428
      nhomalt_popmax: 0
    - cohort: controls
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 2570
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 1164
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 1406
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 246
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 120
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 126
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 38
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 24
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 14
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 914
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 342
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 572
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_oea
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_kor
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: fin
          counts:
            overall:
              ac: 0
              an: 1162
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 556
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 606
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 5518
              nhomalt: 0
              af: 0.000181225
            xx:
              ac: 1
              an: 2576
              nhomalt: 0
              af: 0.000388199
            xy:
              ac: 0
              an: 2942
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_est
          counts:
            overall:
              ac: 0
              an: 4104
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_nwe
          counts:
            overall:
              ac: 0
              an: 920
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_onf
          counts:
            overall:
              ac: 0
              an: 438
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_seu
          counts:
            overall:
              ac: 1
              an: 56
              nhomalt: 0
              af: 0.0178571
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_swe
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: oth
          counts:
            overall:
              ac: 0
              an: 424
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 226
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 198
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
      by_sex:
        overall:
          ac: 1
          an: 10872
          nhomalt: 0
          af: 0.0000919794
        xx:
          ac: 1
          an: 5008
          nhomalt: 0
          af: 0.000199681
        xy:
          ac: 0
          an: 5864
          nhomalt: 0
          af: 0
      raw:
        ac: 1
        an: 10884
        nhomalt: 0
        af: 0.000091878
      popmax: nfe
      af_popmax: 0.000181225
      ac_popmax: 1
      an_popmax: 5518
      nhomalt_popmax: 0
    - cohort: non_cancer
      by_population:
        - population: afr
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_oea
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_kor
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: fin
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_est
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_nwe
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_onf
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_seu
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_swe
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: oth
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
      by_sex:
        overall: ~
        xx: ~
        xy: ~
      raw: ~
      popmax: ~
      af_popmax: ~
      ac_popmax: ~
      an_popmax: ~
      nhomalt_popmax: ~
    - cohort: non_neuro
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 3384
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 1778
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 1606
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 554
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 310
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 244
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 246
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 60
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 186
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 1558
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 538
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 1020
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_oea
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_kor
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: fin
          counts:
            overall:
              ac: 0
              an: 1164
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 558
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 606
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 13618
              nhomalt: 0
              af: 0.0000734322
            xx:
              ac: 1
              an: 5982
              nhomalt: 0
              af: 0.000167168
            xy:
              ac: 0
              an: 7636
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_est
          counts:
            overall:
              ac: 0
              an: 4146
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_nwe
          counts:
            overall:
              ac: 0
              an: 7698
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_onf
          counts:
            overall:
              ac: 0
              an: 1720
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_seu
          counts:
            overall:
              ac: 1
              an: 54
              nhomalt: 0
              af: 0.0185185
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_swe
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: oth
          counts:
            overall:
              ac: 0
              an: 734
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 364
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 370
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
      by_sex:
        overall:
          ac: 1
          an: 21258
          nhomalt: 0
          af: 0.0000470411
        xx:
          ac: 1
          an: 9590
          nhomalt: 0
          af: 0.000104275
        xy:
          ac: 0
          an: 11668
          nhomalt: 0
          af: 0
      raw:
        ac: 1
        an: 21272
        nhomalt: 0
        af: 0.0000470102
      popmax: nfe
      af_popmax: 0.0000734322
      ac_popmax: 1
      an_popmax: 13618
      nhomalt_popmax: 0
    - cohort: non_topmed
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 8544
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 3610
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 4934
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 810
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 394
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 416
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 138
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 62
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 76
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 1520
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 520
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 1000
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_oea
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_kor
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: fin
          counts:
            overall:
              ac: 0
              an: 3476
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 1846
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 1630
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 11088
              nhomalt: 0
              af: 0.0000901876
            xx:
              ac: 1
              an: 5610
              nhomalt: 0
              af: 0.000178253
            xy:
              ac: 0
              an: 5478
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_est
          counts:
            overall:
              ac: 0
              an: 4570
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_nwe
          counts:
            overall:
              ac: 0
              an: 4898
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_onf
          counts:
            overall:
              ac: 0
              an: 1514
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_seu
          counts:
            overall:
              ac: 1
              an: 106
              nhomalt: 0
              af: 0.00943396
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_swe
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: oth
          counts:
            overall:
              ac: 0
              an: 1010
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 544
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 466
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
      by_sex:
        overall:
          ac: 1
          an: 26586
          nhomalt: 0
          af: 0.0000376138
        xx:
          ac: 1
          an: 12586
          nhomalt: 0
          af: 0.0000794534
        xy:
          ac: 0
          an: 14000
          nhomalt: 0
          af: 0
      raw:
        ac: 1
        an: 26608
        nhomalt: 0
        af: 0.0000375827
      popmax: nfe
      af_popmax: 0.0000901876
      ac_popmax: 1
      an_popmax: 11088
      nhomalt_popmax: 0
  nonpar: false
  liftover_info: ~
  rf_info:
    rf_tp_probability: 0.77474
    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: 1.515
    inbreeding_coeff: 0.0198
    mq: 59.95
    mq_rank_sum: -1.385
    qd: 12.71
    read_pos_rank_sum: 0.308
    vqsr_positive_train_site: false
    vqsr_negative_train_site: true
    base_q_rank_sum: 2.21
    clipping_rank_sum: 1.33
    sor: 1.022
    dp: 696568
    vqslod: -2.305
    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: 2
    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: 154
              an: 8702
              nhomalt: 0
              af: 0.0176971
            xx:
              ac: 67
              an: 3674
              nhomalt: 0
              af: 0.0182363
            xy:
              ac: 87
              an: 5028
              nhomalt: 0
              af: 0.0173031
          faf95: 0.0154185
          faf99: 0.0154183
        - population: amr
          counts:
            overall:
              ac: 0
              an: 848
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 414
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 434
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 290
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 80
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 210
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 1560
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 538
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 1022
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_oea
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_kor
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: fin
          counts:
            overall:
              ac: 0
              an: 3476
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 1846
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 1630
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 15420
              nhomalt: 0
              af: 0.0000648508
            xx:
              ac: 0
              an: 6800
              nhomalt: 0
              af: 0
            xy:
              ac: 1
              an: 8620
              nhomalt: 0
              af: 0.000116009
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_est
          counts:
            overall:
              ac: 0
              an: 4584
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_nwe
          counts:
            overall:
              ac: 1
              an: 8592
              nhomalt: 0
              af: 0.000116387
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_onf
          counts:
            overall:
              ac: 0
              an: 2138
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_seu
          counts:
            overall:
              ac: 0
              an: 106
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_swe
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: oth
          counts:
            overall:
              ac: 1
              an: 1086
              nhomalt: 0
              af: 0.00092081
            xx:
              ac: 0
              an: 560
              nhomalt: 0
              af: 0
            xy:
              ac: 1
              an: 526
              nhomalt: 0
              af: 0.00190114
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
      by_sex:
        overall:
          ac: 156
          an: 31382
          nhomalt: 0
          af: 0.004971
        xx:
          ac: 67
          an: 13912
          nhomalt: 0
          af: 0.00481599
        xy:
          ac: 89
          an: 17470
          nhomalt: 0
          af: 0.00509445
      raw:
        ac: 156
        an: 31416
        nhomalt: 0
        af: 0.00496562
      popmax: afr
      af_popmax: 0.0176971
      ac_popmax: 154
      an_popmax: 8702
      nhomalt_popmax: 0
    - cohort: controls
      by_population:
        - population: afr
          counts:
            overall:
              ac: 40
              an: 2572
              nhomalt: 0
              af: 0.0155521
            xx:
              ac: 25
              an: 1164
              nhomalt: 0
              af: 0.0214777
            xy:
              ac: 15
              an: 1408
              nhomalt: 0
              af: 0.0106534
          faf95: 0.0154185
          faf99: 0.0154183
        - population: amr
          counts:
            overall:
              ac: 0
              an: 246
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 120
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 126
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 38
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 24
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 14
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 916
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 342
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 574
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_oea
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_kor
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: fin
          counts:
            overall:
              ac: 0
              an: 1162
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 556
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 606
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 0
              an: 5514
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 2576
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 2938
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_est
          counts:
            overall:
              ac: 0
              an: 4096
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_nwe
          counts:
            overall:
              ac: 0
              an: 922
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_onf
          counts:
            overall:
              ac: 0
              an: 440
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_seu
          counts:
            overall:
              ac: 0
              an: 56
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_swe
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: oth
          counts:
            overall:
              ac: 0
              an: 422
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 224
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 198
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
      by_sex:
        overall:
          ac: 40
          an: 10870
          nhomalt: 0
          af: 0.00367985
        xx:
          ac: 25
          an: 5006
          nhomalt: 0
          af: 0.00499401
        xy:
          ac: 15
          an: 5864
          nhomalt: 0
          af: 0.00255798
      raw:
        ac: 40
        an: 10884
        nhomalt: 0
        af: 0.00367512
      popmax: afr
      af_popmax: 0.0155521
      ac_popmax: 40
      an_popmax: 2572
      nhomalt_popmax: 0
    - cohort: non_cancer
      by_population:
        - population: afr
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: 0.0154185
          faf99: 0.0154183
        - population: amr
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_oea
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_kor
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: fin
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_est
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_nwe
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_onf
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_seu
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_swe
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: oth
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
      by_sex:
        overall: ~
        xx: ~
        xy: ~
      raw: ~
      popmax: ~
      af_popmax: ~
      ac_popmax: ~
      an_popmax: ~
      nhomalt_popmax: ~
    - cohort: non_neuro
      by_population:
        - population: afr
          counts:
            overall:
              ac: 48
              an: 3386
              nhomalt: 0
              af: 0.014176
            xx:
              ac: 31
              an: 1778
              nhomalt: 0
              af: 0.0174353
            xy:
              ac: 17
              an: 1608
              nhomalt: 0
              af: 0.0105721
          faf95: 0.0154185
          faf99: 0.0154183
        - population: amr
          counts:
            overall:
              ac: 0
              an: 554
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 310
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 244
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 246
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 60
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 186
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 1560
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 538
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 1022
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_oea
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_kor
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: fin
          counts:
            overall:
              ac: 0
              an: 1164
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 558
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 606
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 13610
              nhomalt: 0
              af: 0.0000734754
            xx:
              ac: 0
              an: 5976
              nhomalt: 0
              af: 0
            xy:
              ac: 1
              an: 7634
              nhomalt: 0
              af: 0.000130993
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_est
          counts:
            overall:
              ac: 0
              an: 4138
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_nwe
          counts:
            overall:
              ac: 1
              an: 7696
              nhomalt: 0
              af: 0.000129938
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_onf
          counts:
            overall:
              ac: 0
              an: 1722
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_seu
          counts:
            overall:
              ac: 0
              an: 54
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_swe
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: oth
          counts:
            overall:
              ac: 0
              an: 732
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 362
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 370
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
      by_sex:
        overall:
          ac: 49
          an: 21252
          nhomalt: 0
          af: 0.00230567
        xx:
          ac: 31
          an: 9582
          nhomalt: 0
          af: 0.00323523
        xy:
          ac: 18
          an: 11670
          nhomalt: 0
          af: 0.00154242
      raw:
        ac: 49
        an: 21272
        nhomalt: 0
        af: 0.0023035
      popmax: afr
      af_popmax: 0.014176
      ac_popmax: 48
      an_popmax: 3386
      nhomalt_popmax: 0
    - cohort: non_topmed
      by_population:
        - population: afr
          counts:
            overall:
              ac: 152
              an: 8540
              nhomalt: 0
              af: 0.0177986
            xx:
              ac: 66
              an: 3606
              nhomalt: 0
              af: 0.0183028
            xy:
              ac: 86
              an: 4934
              nhomalt: 0
              af: 0.0174301
          faf95: 0.0154185
          faf99: 0.0154183
        - population: amr
          counts:
            overall:
              ac: 0
              an: 810
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 394
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 416
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 138
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 62
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 76
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 1522
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 520
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 1002
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_oea
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_kor
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: fin
          counts:
            overall:
              ac: 0
              an: 3476
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 1846
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 1630
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 11080
              nhomalt: 0
              af: 0.0000902527
            xx:
              ac: 0
              an: 5606
              nhomalt: 0
              af: 0
            xy:
              ac: 1
              an: 5474
              nhomalt: 0
              af: 0.000182682
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_est
          counts:
            overall:
              ac: 0
              an: 4562
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_nwe
          counts:
            overall:
              ac: 1
              an: 4896
              nhomalt: 0
              af: 0.000204248
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_onf
          counts:
            overall:
              ac: 0
              an: 1516
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_seu
          counts:
            overall:
              ac: 0
              an: 106
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_swe
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: oth
          counts:
            overall:
              ac: 1
              an: 1010
              nhomalt: 0
              af: 0.000990099
            xx:
              ac: 0
              an: 544
              nhomalt: 0
              af: 0
            xy:
              ac: 1
              an: 466
              nhomalt: 0
              af: 0.00214592
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
      by_sex:
        overall:
          ac: 154
          an: 26576
          nhomalt: 0
          af: 0.0057947
        xx:
          ac: 66
          an: 12578
          nhomalt: 0
          af: 0.00524726
        xy:
          ac: 88
          an: 13998
          nhomalt: 0
          af: 0.00628661
      raw:
        ac: 154
        an: 26608
        nhomalt: 0
        af: 0.00578773
      popmax: afr
      af_popmax: 0.0177986
      ac_popmax: 152
      an_popmax: 8540
      nhomalt_popmax: 0
  nonpar: false
  liftover_info: ~
  rf_info:
    rf_tp_probability: 0.952127
    rf_positive_label: true
    rf_negative_label: false
    rf_label: TP
    rf_train: true
  variant_info:
    variant_type: indel
    allele_type: ins
    n_alt_alleles: 1
    was_mixed: false
    has_star: false
  quality_info:
    fs: 0.52
    inbreeding_coeff: -0.0043
    mq: 60
    mq_rank_sum: -0.017
    qd: 15.91
    read_pos_rank_sum: 0.122
    vqsr_positive_train_site: true
    vqsr_negative_train_site: false
    base_q_rank_sum: -0.161
    clipping_rank_sum: -0.129
    sor: 0.654
    dp: 660105
    vqslod: 4.41
    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: 64
    age_hist_het_n_larger: 2
  depth_info:
    dp_hist_all_n_larger: 1
    dp_hist_alt_n_larger: 0
    dp_hist_all_bin_freq: []
    dp_hist_alt_bin_freq: []
- chrom: X
  pos: 69902634
  ref_allele: C
  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.1091G>A"
      hgvsp: "ENSP00000340995.3:p.Arg364His"
      cdna_position: "1091"
      cds_position: "1091"
      protein_position: "364"
      amino_acids: R/H
      codons: cGt/cAt
      existing_variation: rs201471690
      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: 1
      polyphen:
        prediction: benign
        score: 0.007
      domains:
        - id: PTHR22904
          source: hmmpanther
        - id: PTHR22904
          source: hmmpanther
        - id: PF08631
          source: Pfam_domain
      hgvs_offset: ~
      gmaf: 0.0005
      afr_maf: 0
      amr_maf: 0.0008
      eas_maf: 0
      eur_maf: 0
      sas_maf: 0.001
      aa_maf: 0
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: 0
      exac_afr_maf: 0.00003295
      exac_amr_maf: 0.0001237
      exac_eas_maf: 0.00002495
      exac_fin_maf: 0
      exac_nfe_maf: 0
      exac_oth_maf: 0.00002306
      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:69902524&EXON_END:69902675&DE_NOVO_DONOR_MES:0.0381663094165419&DE_NOVO_DONOR_POS:-108&DE_NOVO_DONOR_MES_POS:-108&MUTANT_DONOR_MES:6.38837132164763&DE_NOVO_DONOR_PROB:0.0218748740634797&INTRON_END:69902523&INTRON_START:69898740"
    - 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.116G>A"
      hgvsp: "ENSP00000363440.2:p.Arg39His"
      cdna_position: "338"
      cds_position: "116"
      protein_position: "39"
      amino_acids: R/H
      codons: cGt/cAt
      existing_variation: rs201471690
      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: 1
      polyphen:
        prediction: benign
        score: 0.007
      domains:
        - id: PTHR22904
          source: hmmpanther
        - id: PTHR22904
          source: hmmpanther
        - id: PF08631
          source: Pfam_domain
      hgvs_offset: ~
      gmaf: 0.0005
      afr_maf: 0
      amr_maf: 0.0008
      eas_maf: 0
      eur_maf: 0
      sas_maf: 0.001
      aa_maf: 0
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: 0
      exac_afr_maf: 0.00003295
      exac_amr_maf: 0.0001237
      exac_eas_maf: 0.00002495
      exac_fin_maf: 0
      exac_nfe_maf: 0
      exac_oth_maf: 0.00002306
      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: "INTRON_END:69902523&DE_NOVO_DONOR_PROB:0.0218748740634797&MUTANT_DONOR_MES:6.38837132164763&INTRON_START:69898740&EXON_START:69902524&EXON_END:69902675&DE_NOVO_DONOR_MES:0.0381663094165419&DE_NOVO_DONOR_POS:-108&DE_NOVO_DONOR_MES_POS:-108"
    - 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.1046G>A"
      hgvsp: "ENSP00000363453.2:p.Arg349His"
      cdna_position: "1145"
      cds_position: "1046"
      protein_position: "349"
      amino_acids: R/H
      codons: cGt/cAt
      existing_variation: rs201471690
      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: 1
      polyphen:
        prediction: benign
        score: 0.003
      domains:
        - id: PTHR22904
          source: hmmpanther
        - id: PTHR22904
          source: hmmpanther
        - id: PF08631
          source: Pfam_domain
      hgvs_offset: ~
      gmaf: 0.0005
      afr_maf: 0
      amr_maf: 0.0008
      eas_maf: 0
      eur_maf: 0
      sas_maf: 0.001
      aa_maf: 0
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: 0
      exac_afr_maf: 0.00003295
      exac_amr_maf: 0.0001237
      exac_eas_maf: 0.00002495
      exac_fin_maf: 0
      exac_nfe_maf: 0
      exac_oth_maf: 0.00002306
      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_POS:-108&DE_NOVO_DONOR_MES_POS:-108&EXON_START:69902524&EXON_END:69902675&DE_NOVO_DONOR_MES:0.0381663094165419&INTRON_START:69898740&INTRON_END:69902523&DE_NOVO_DONOR_PROB:0.0218748740634797&MUTANT_DONOR_MES:6.38837132164763"
    - 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.1091G>A"
      hgvsp: "ENSP00000379226.2:p.Arg364His"
      cdna_position: "1247"
      cds_position: "1091"
      protein_position: "364"
      amino_acids: R/H
      codons: cGt/cAt
      existing_variation: rs201471690
      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: 1
      polyphen:
        prediction: benign
        score: 0.007
      domains:
        - id: PTHR22904
          source: hmmpanther
        - id: PTHR22904
          source: hmmpanther
        - id: PF08631
          source: Pfam_domain
      hgvs_offset: ~
      gmaf: 0.0005
      afr_maf: 0
      amr_maf: 0.0008
      eas_maf: 0
      eur_maf: 0
      sas_maf: 0.001
      aa_maf: 0
      ea_maf: ~
      exac_maf: ~
      exac_adj_maf: 0
      exac_afr_maf: 0.00003295
      exac_amr_maf: 0.0001237
      exac_eas_maf: 0.00002495
      exac_fin_maf: 0
      exac_nfe_maf: 0
      exac_oth_maf: 0.00002306
      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: "INTRON_END:69902523&DE_NOVO_DONOR_PROB:0.0218748740634797&MUTANT_DONOR_MES:6.38837132164763&INTRON_START:69898740&EXON_END:69902675&EXON_START:69902524&DE_NOVO_DONOR_MES:0.0381663094165419&DE_NOVO_DONOR_POS:-108&DE_NOVO_DONOR_MES_POS:-108"
  allele_counts:
    - cohort: ~
      by_population:
        - population: afr
          counts:
            overall:
              ac: 1
              an: 5881
              nhomalt: 0
              af: 0.000170039
            xx:
              ac: 1
              an: 3682
              nhomalt: 0
              af: 0.000271592
            xy:
              ac: 0
              an: 2199
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 612
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 414
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 198
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 175
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 80
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 95
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 1008
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 538
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 470
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_oea
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_kor
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: fin
          counts:
            overall:
              ac: 0
              an: 2574
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 1844
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 730
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 0
              an: 10810
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 6806
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 4004
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_est
          counts:
            overall:
              ac: 0
              an: 3312
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_nwe
          counts:
            overall:
              ac: 0
              an: 5938
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_onf
          counts:
            overall:
              ac: 0
              an: 1486
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_seu
          counts:
            overall:
              ac: 0
              an: 74
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_swe
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: oth
          counts:
            overall:
              ac: 0
              an: 797
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 562
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 235
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
      by_sex:
        overall:
          ac: 1
          an: 21857
          nhomalt: 0
          af: 0.0000457519
        xx:
          ac: 1
          an: 13926
          nhomalt: 0
          af: 0.0000718081
        xy:
          ac: 0
          an: 7931
          nhomalt: 0
          af: 0
      raw:
        ac: 1
        an: 22675
        nhomalt: 0
        af: 0.0000441014
      popmax: afr
      af_popmax: 0.000170039
      ac_popmax: 1
      an_popmax: 5881
      nhomalt_popmax: 0
    - cohort: controls
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 1779
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 1166
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 613
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 177
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 120
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 57
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 31
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 24
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 7
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 611
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 342
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 269
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_oea
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_kor
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: fin
          counts:
            overall:
              ac: 0
              an: 828
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 554
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 274
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 0
              an: 3888
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 2578
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 1310
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_est
          counts:
            overall:
              ac: 0
              an: 2928
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_nwe
          counts:
            overall:
              ac: 0
              an: 610
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_onf
          counts:
            overall:
              ac: 0
              an: 310
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_seu
          counts:
            overall:
              ac: 0
              an: 40
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_swe
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: oth
          counts:
            overall:
              ac: 0
              an: 313
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 226
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 87
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
      by_sex:
        overall:
          ac: 0
          an: 7627
          nhomalt: 0
          af: 0
        xx:
          ac: 0
          an: 5010
          nhomalt: 0
          af: 0
        xy:
          ac: 0
          an: 2617
          nhomalt: 0
          af: 0
      raw:
        ac: 0
        an: 7950
        nhomalt: 0
        af: 0
      popmax: ~
      af_popmax: ~
      ac_popmax: ~
      an_popmax: ~
      nhomalt_popmax: ~
    - cohort: non_cancer
      by_population:
        - population: afr
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_oea
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_kor
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: fin
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_est
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_nwe
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_onf
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_seu
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_swe
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: oth
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
      by_sex:
        overall: ~
        xx: ~
        xy: ~
      raw: ~
      popmax: ~
      af_popmax: ~
      ac_popmax: ~
      an_popmax: ~
      nhomalt_popmax: ~
    - cohort: non_neuro
      by_population:
        - population: afr
          counts:
            overall:
              ac: 0
              an: 2486
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 1780
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 706
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 420
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 310
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 110
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 148
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 60
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 88
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 1008
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 538
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 470
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_oea
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_kor
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: fin
          counts:
            overall:
              ac: 0
              an: 830
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 556
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 274
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 0
              an: 9531
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 5982
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 3549
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_est
          counts:
            overall:
              ac: 0
              an: 2957
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_nwe
          counts:
            overall:
              ac: 0
              an: 5329
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_onf
          counts:
            overall:
              ac: 0
              an: 1206
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_seu
          counts:
            overall:
              ac: 0
              an: 39
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_swe
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: oth
          counts:
            overall:
              ac: 0
              an: 526
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 364
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 162
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
      by_sex:
        overall:
          ac: 0
          an: 14949
          nhomalt: 0
          af: 0
        xx:
          ac: 0
          an: 9590
          nhomalt: 0
          af: 0
        xy:
          ac: 0
          an: 5359
          nhomalt: 0
          af: 0
      raw:
        ac: 0
        an: 15435
        nhomalt: 0
        af: 0
      popmax: ~
      af_popmax: ~
      ac_popmax: ~
      an_popmax: ~
      nhomalt_popmax: ~
    - cohort: non_topmed
      by_population:
        - population: afr
          counts:
            overall:
              ac: 1
              an: 5767
              nhomalt: 0
              af: 0.0001734
            xx:
              ac: 1
              an: 3614
              nhomalt: 0
              af: 0.000276702
            xy:
              ac: 0
              an: 2153
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 0
              an: 583
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 394
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 189
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              ac: 0
              an: 93
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 62
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 31
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: eas
          counts:
            overall:
              ac: 0
              an: 981
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 520
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 461
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_oea
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: eas_kor
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: fin
          counts:
            overall:
              ac: 0
              an: 2574
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 1844
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 730
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: nfe
          counts:
            overall:
              ac: 0
              an: 8098
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 5610
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 2488
              nhomalt: 0
              af: 0
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_est
          counts:
            overall:
              ac: 0
              an: 3297
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_nwe
          counts:
            overall:
              ac: 0
              an: 3627
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_onf
          counts:
            overall:
              ac: 0
              an: 1100
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_seu
          counts:
            overall:
              ac: 0
              an: 74
              nhomalt: 0
              af: 0
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: nfe_swe
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
        - population: oth
          counts:
            overall:
              ac: 0
              an: 752
              nhomalt: 0
              af: 0
            xx:
              ac: 0
              an: 546
              nhomalt: 0
              af: 0
            xy:
              ac: 0
              an: 206
              nhomalt: 0
              af: 0
          faf95: ~
          faf99: ~
        - population: sas
          counts:
            overall: ~
            xx: ~
            xy: ~
          faf95: ~
          faf99: ~
      by_sex:
        overall:
          ac: 1
          an: 18848
          nhomalt: 0
          af: 0.000053056
        xx:
          ac: 1
          an: 12590
          nhomalt: 0
          af: 0.0000794281
        xy:
          ac: 0
          an: 6258
          nhomalt: 0
          af: 0
      raw:
        ac: 1
        an: 19603
        nhomalt: 0
        af: 0.0000510126
      popmax: afr
      af_popmax: 0.0001734
      ac_popmax: 1
      an_popmax: 5767
      nhomalt_popmax: 0
  nonpar: true
  liftover_info: ~
  rf_info:
    rf_tp_probability: 0.208912
    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: 3.617
    inbreeding_coeff: -0.0007
    mq: 60
    mq_rank_sum: 0.344
    qd: 4.62
    read_pos_rank_sum: 1.23
    vqsr_positive_train_site: false
    vqsr_negative_train_site: false
    base_q_rank_sum: 1.87
    clipping_rank_sum: 1.62
    sor: 1.358
    dp: 464079
    vqslod: 13.71
    vqsr_culprit: MQ
    segdup: false
    lcr: false
    decoy: false
    transmitted_singleton: false
    pab_max: 0.0871586
  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: 1
    age_hist_het_n_larger: 0
  depth_info:
    dp_hist_all_n_larger: 0
    dp_hist_alt_n_larger: 0
    dp_hist_all_bin_freq: []
    dp_hist_alt_bin_freq: []

