---
source: src/pbs/gnomad/gnomad2.rs
expression: records
---
- chrom: "1"
  pos: 55505599
  refAllele: C
  altAllele: G
  vep:
    - allele: G
      consequence: missense_variant
      impact: MODERATE
      symbol: PCSK9
      gene: ENSG00000169174
      featureType: Transcript
      feature: ENST00000302118
      featureBiotype: protein_coding
      exon: 1/12
      hgvsc: "ENST00000302118.5:c.89C>G"
      hgvsp: "ENSP00000303208.5:p.Ala30Gly"
      cdnaPosition: "379"
      cdsPosition: "89"
      proteinPosition: "30"
      aminoAcids: A/G
      codons: gCg/gGg
      dbsnpId: "1"
      strand: "1"
      variantClass: SNV
      minimised: "1"
      symbolSource: HGNC
      hgncId: "20001"
      canonical: true
      ccds: CCDS603.1
      ensp: ENSP00000303208
      swissprot: Q8NBP7
      uniparc: UPI00001615E1
      genePheno: "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
      lofInfo: "DE_NOVO_DONOR_PROB:0.146539915246404&MUTANT_DONOR_MES:8.16693067332728&DE_NOVO_DONOR_POS:-119&INTRON_END:55509515&DE_NOVO_DONOR_MES_POS:-122&INTRON_START:55505718&EXON_END:55505717&EXON_START:55505221&DE_NOVO_DONOR_MES:-1.61109392005567"
    - allele: G
      consequence: missense_variant
      impact: MODERATE
      symbol: PCSK9
      gene: ENSG00000169174
      featureType: Transcript
      feature: ENST00000452118
      featureBiotype: protein_coding
      exon: 1/6
      hgvsc: "ENST00000452118.2:c.89C>G"
      hgvsp: "ENSP00000401598.2:p.Ala30Gly"
      cdnaPosition: "169"
      cdsPosition: "89"
      proteinPosition: "30"
      aminoAcids: A/G
      codons: gCg/gGg
      dbsnpId: "1"
      strand: "1"
      variantClass: SNV
      minimised: "1"
      symbolSource: HGNC
      hgncId: "20001"
      ensp: ENSP00000401598
      trembl: B4DEZ9
      uniparc: UPI00017A6F55
      genePheno: "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
      lofInfo: "DE_NOVO_DONOR_MES_POS:-122&INTRON_START:55505718&INTRON_END:55509515&EXON_START:55505431&DE_NOVO_DONOR_MES:-1.61109392005567&EXON_END:55505717&MUTANT_DONOR_MES:8.16693067332728&DE_NOVO_DONOR_PROB:0.146539915246404&DE_NOVO_DONOR_POS:-119"
    - allele: G
      consequence: upstream_gene_variant
      impact: MODIFIER
      symbol: PCSK9
      gene: ENSG00000169174
      featureType: Transcript
      feature: ENST00000543384
      featureBiotype: protein_coding
      dbsnpId: "1"
      distance: "296"
      strand: "1"
      variantClass: SNV
      minimised: "1"
      symbolSource: HGNC
      hgncId: "20001"
      ensp: ENSP00000441859
      trembl: F5GWF0
      uniparc: UPI000206501F
      genePheno: "1"
    - allele: G
      consequence: regulatory_region_variant
      impact: MODIFIER
      featureType: RegulatoryFeature
      feature: ENSR00001037993
      featureBiotype: promoter
      dbsnpId: "1"
      variantClass: SNV
      minimised: "1"
  alleleCounts:
    - byPopulation:
        - population: afr
          counts:
            overall:
              an: 10278
            xx:
              an: 6396
            xy:
              an: 3882
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 26912
            xx:
              an: 15498
            xy:
              an: 11414
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 8820
            xx:
              an: 4180
            xy:
              an: 4640
        - population: eas
          counts:
            overall:
              an: 13152
            xx:
              an: 6510
            xy:
              an: 6642
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 62
        - population: eas_oea
          counts:
            overall:
              an: 10220
        - population: eas_kor
          counts:
            overall:
              an: 2870
        - population: fin
          counts:
            overall:
              an: 16514
            xx:
              an: 8530
            xy:
              an: 7984
        - population: nfe
          counts:
            overall:
              ac: 2
              an: 74572
              af: 0.0000268197
            xx:
              ac: 1
              an: 33698
              af: 0.0000296754
            xy:
              ac: 1
              an: 40874
              af: 0.0000244654
          faf95: 0.00000445
          faf99: 0.00000467
        - population: nfe_bgr
          counts:
            overall:
              an: 1356
        - population: nfe_est
          counts:
            overall:
              an: 208
        - population: nfe_nwe
          counts:
            overall:
              ac: 2
              an: 36842
              af: 0.0000542859
        - population: nfe_onf
          counts:
            overall:
              an: 21582
        - population: nfe_seu
          counts:
            overall:
              an: 4056
        - population: nfe_swe
          counts:
            overall:
              an: 10528
        - population: oth
          counts:
            overall:
              an: 4864
            xx:
              an: 2342
            xy:
              an: 2522
        - population: sas
          counts:
            overall:
              an: 24186
            xx:
              an: 6130
            xy:
              an: 18056
          faf95: 0
          faf99: 0
      bySex:
        overall:
          ac: 2
          an: 179298
          af: 0.0000111546
        xx:
          ac: 1
          an: 83284
          af: 0.0000120071
        xy:
          ac: 1
          an: 96014
          af: 0.0000104151
      raw:
        ac: 2
        an: 250244
        af: 0.0000079922
      popmax: nfe
      afPopmax: 0.0000268197
      acPopmax: 2
      anPopmax: 74572
      nhomaltPopmax: 0
    - cohort: controls
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 3706
            xx:
              an: 2086
            xy:
              an: 1620
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 13388
            xx:
              an: 7848
            xy:
              an: 5540
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 1628
            xx:
              an: 812
            xy:
              an: 816
        - population: eas
          counts:
            overall:
              an: 5546
            xx:
              an: 2836
            xy:
              an: 2710
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 34
        - population: eas_oea
          counts:
            overall:
              an: 4096
        - population: eas_kor
          counts:
            overall:
              an: 1416
        - population: fin
          counts:
            overall:
              an: 11740
            xx:
              an: 6008
            xy:
              an: 5732
        - population: nfe
          counts:
            overall:
              ac: 2
              an: 26960
              af: 0.000074184
            xx:
              ac: 1
              an: 12126
              af: 0.0000824674
            xy:
              ac: 1
              an: 14834
              af: 0.0000674127
          faf95: 0.00000445
          faf99: 0.00000467
        - population: nfe_bgr
          counts:
            overall:
              an: 206
        - population: nfe_est
          counts:
            overall:
              an: 64
        - population: nfe_nwe
          counts:
            overall:
              ac: 2
              an: 12958
              af: 0.000154345
        - population: nfe_onf
          counts:
            overall:
              an: 7146
        - population: nfe_seu
          counts:
            overall:
              an: 1408
        - population: nfe_swe
          counts:
            overall:
              an: 5178
        - population: oth
          counts:
            overall:
              an: 1500
            xx:
              an: 748
            xy:
              an: 752
        - population: sas
          counts:
            overall:
              an: 12070
            xx:
              an: 3364
            xy:
              an: 8706
          faf95: 0
          faf99: 0
      bySex:
        overall:
          ac: 2
          an: 76538
          af: 0.0000261308
        xx:
          ac: 1
          an: 35828
          af: 0.0000279111
        xy:
          ac: 1
          an: 40710
          af: 0.000024564
      raw:
        ac: 2
        an: 108948
        af: 0.0000183574
      popmax: nfe
      afPopmax: 0.000074184
      acPopmax: 2
      anPopmax: 26960
      nhomaltPopmax: 0
    - cohort: non_cancer
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 9588
            xx:
              an: 5892
            xy:
              an: 3696
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 26772
            xx:
              an: 15412
            xy:
              an: 11360
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 8582
            xx:
              an: 4050
            xy:
              an: 4532
        - population: eas
          counts:
            overall:
              an: 12820
            xx:
              an: 6314
            xy:
              an: 6506
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 44
        - population: eas_oea
          counts:
            overall:
              an: 9922
        - population: eas_kor
          counts:
            overall:
              an: 2854
        - population: fin
          counts:
            overall:
              an: 16508
            xx:
              an: 8526
            xy:
              an: 7982
        - population: nfe
          counts:
            overall:
              ac: 2
              an: 69892
              af: 0.0000286156
            xx:
              ac: 1
              an: 30948
              af: 0.0000323123
            xy:
              ac: 1
              an: 38944
              af: 0.0000256779
          faf95: 0.00000445
          faf99: 0.00000467
        - population: nfe_bgr
          counts:
            overall:
              an: 1312
        - population: nfe_est
          counts:
            overall:
              an: 150
        - population: nfe_nwe
          counts:
            overall:
              ac: 2
              an: 35322
              af: 0.0000566219
        - population: nfe_onf
          counts:
            overall:
              an: 19112
        - population: nfe_seu
          counts:
            overall:
              an: 3716
        - population: nfe_swe
          counts:
            overall:
              an: 10280
        - population: oth
          counts:
            overall:
              an: 4670
            xx:
              an: 2236
            xy:
              an: 2434
        - population: sas
          counts:
            overall:
              an: 24158
            xx:
              an: 6112
            xy:
              an: 18046
          faf95: 0
          faf99: 0
      bySex:
        overall:
          ac: 2
          an: 172990
          af: 0.0000115614
        xx:
          ac: 1
          an: 79490
          af: 0.0000125802
        xy:
          ac: 1
          an: 93500
          af: 0.0000106952
      raw:
        ac: 2
        an: 236048
        af: 0.00000847285
      popmax: nfe
      afPopmax: 0.0000286156
      acPopmax: 2
      anPopmax: 69892
      nhomaltPopmax: 0
    - cohort: non_neuro
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 10242
            xx:
              an: 6380
            xy:
              an: 3862
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 22850
            xx:
              an: 13496
            xy:
              an: 9354
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 5026
            xx:
              an: 2404
            xy:
              an: 2622
        - population: eas
          counts:
            overall:
              an: 10236
            xx:
              an: 5050
            xy:
              an: 5186
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 60
        - population: eas_oea
          counts:
            overall:
              an: 7308
        - population: eas_kor
          counts:
            overall:
              an: 2868
        - population: fin
          counts:
            overall:
              an: 13938
            xx:
              an: 7000
            xy:
              an: 6938
        - population: nfe
          counts:
            overall:
              ac: 2
              an: 59746
              af: 0.000033475
            xx:
              ac: 1
              an: 27742
              af: 0.0000360464
            xy:
              ac: 1
              an: 32004
              af: 0.0000312461
          faf95: 0.00000445
          faf99: 0.00000467
        - population: nfe_bgr
          counts:
            overall:
              an: 298
        - population: nfe_est
          counts:
            overall:
              an: 182
        - population: nfe_nwe
          counts:
            overall:
              ac: 2
              an: 30148
              af: 0.0000663394
        - population: nfe_onf
          counts:
            overall:
              an: 18854
        - population: nfe_seu
          counts:
            overall:
              an: 3576
        - population: nfe_swe
          counts:
            overall:
              an: 6688
        - population: oth
          counts:
            overall:
              an: 3880
            xx:
              an: 1920
            xy:
              an: 1960
        - population: sas
          counts:
            overall:
              an: 24180
            xx:
              an: 6130
            xy:
              an: 18050
          faf95: 0
          faf99: 0
      bySex:
        overall:
          ac: 2
          an: 150098
          af: 0.0000133246
        xx:
          ac: 1
          an: 70122
          af: 0.0000142609
        xy:
          ac: 1
          an: 79976
          af: 0.0000125038
      raw:
        ac: 2
        an: 207100
        af: 0.00000965717
      popmax: nfe
      afPopmax: 0.000033475
      acPopmax: 2
      anPopmax: 59746
      nhomaltPopmax: 0
    - cohort: non_topmed
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 9010
            xx:
              an: 5548
            xy:
              an: 3462
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 26844
            xx:
              an: 15458
            xy:
              an: 11386
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 8756
            xx:
              an: 4144
            xy:
              an: 4612
        - population: eas
          counts:
            overall:
              an: 13148
            xx:
              an: 6510
            xy:
              an: 6638
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 62
        - population: eas_oea
          counts:
            overall:
              an: 10216
        - population: eas_kor
          counts:
            overall:
              an: 2870
        - population: fin
          counts:
            overall:
              an: 16512
            xx:
              an: 8528
            xy:
              an: 7984
        - population: nfe
          counts:
            overall:
              ac: 2
              an: 72974
              af: 0.000027407
            xx:
              ac: 1
              an: 32716
              af: 0.0000305661
            xy:
              ac: 1
              an: 40258
              af: 0.0000248398
          faf95: 0.00000445
          faf99: 0.00000467
        - population: nfe_bgr
          counts:
            overall:
              an: 1350
        - population: nfe_est
          counts:
            overall:
              an: 204
        - population: nfe_nwe
          counts:
            overall:
              ac: 2
              an: 35840
              af: 0.0000558036
        - population: nfe_onf
          counts:
            overall:
              an: 21056
        - population: nfe_seu
          counts:
            overall:
              an: 4024
        - population: nfe_swe
          counts:
            overall:
              an: 10500
        - population: oth
          counts:
            overall:
              an: 4798
            xx:
              an: 2302
            xy:
              an: 2496
        - population: sas
          counts:
            overall:
              an: 24186
            xx:
              an: 6130
            xy:
              an: 18056
          faf95: 0
          faf99: 0
      bySex:
        overall:
          ac: 2
          an: 176228
          af: 0.0000113489
        xx:
          ac: 1
          an: 81336
          af: 0.0000122947
        xy:
          ac: 1
          an: 94892
          af: 0.0000105383
      raw:
        ac: 2
        an: 243722
        af: 0.00000820607
      popmax: nfe
      afPopmax: 0.000027407
      acPopmax: 2
      anPopmax: 72974
      nhomaltPopmax: 0
  rfInfo:
    rfTpProbability: 0.718866
  variantInfo:
    variantType: snv
    alleleType: snv
    nAltAlleles: 1
  qualityInfo:
    fs: 4.683
    inbreedingCoeff: -0.0078
    mq: 60
    mqRankSum: 0.099
    qd: 12.72
    readPosRankSum: 0.198
    baseQRankSum: -1.495
    clippingRankSum: -0.322
    sor: 0.421
    dp: 9394121
    vqslod: 0.044
    vqsrCulprit: MQ
    pabMax: 1
  ageInfo:
    ageHistHomNSmaller: 0
    ageHistHomNLarger: 0
    ageHistHetNSmaller: 0
    ageHistHetNLarger: 0
  depthInfo:
    dpHistAllNLarger: 13668
    dpHistAltNLarger: 1
- chrom: "1"
  pos: 55505615
  refAllele: C
  altAllele: T
  vep:
    - allele: T
      consequence: synonymous_variant
      impact: LOW
      symbol: PCSK9
      gene: ENSG00000169174
      featureType: Transcript
      feature: ENST00000302118
      featureBiotype: protein_coding
      exon: 1/12
      hgvsc: "ENST00000302118.5:c.105C>T"
      hgvsp: "ENST00000302118.5:c.105C>T(p.=)"
      cdnaPosition: "395"
      cdsPosition: "105"
      proteinPosition: "35"
      aminoAcids: D
      codons: gaC/gaT
      existingVariation: rs533474523
      dbsnpId: "1"
      strand: "1"
      variantClass: SNV
      minimised: "1"
      symbolSource: HGNC
      hgncId: "20001"
      canonical: true
      ccds: CCDS603.1
      ensp: ENSP00000303208
      swissprot: Q8NBP7
      uniparc: UPI00001615E1
      genePheno: "1"
      domains:
        - id: PTHR10795
          source: hmmpanther
        - id: PTHR10795
          source: hmmpanther
      gmaf: 0.0002
      afrMaf: 0.0002414
      amrMaf: 0
      easMaf: 0
      eurMaf: 0
      sasMaf: 0
      aaMaf: 0.001
      exacAdjMaf: 0
      exacAfrMaf: 0.00001679
      exacAmrMaf: 0
      exacEasMaf: 0.00007421
      exacFinMaf: 0
      exacNfeMaf: 0
      exacOthMaf: 0
      exacSasMaf: 0
      lofInfo: "DE_NOVO_DONOR_MES_POS:-106&INTRON_START:55505718&INTRON_END:55509515&EXON_START:55505221&DE_NOVO_DONOR_MES:-4.29805061924569&EXON_END:55505717&MUTANT_DONOR_MES:8.16693067332728&DE_NOVO_DONOR_PROB:0.0706215314144107&DE_NOVO_DONOR_POS:-105"
    - allele: T
      consequence: synonymous_variant
      impact: LOW
      symbol: PCSK9
      gene: ENSG00000169174
      featureType: Transcript
      feature: ENST00000452118
      featureBiotype: protein_coding
      exon: 1/6
      hgvsc: "ENST00000452118.2:c.105C>T"
      hgvsp: "ENST00000452118.2:c.105C>T(p.=)"
      cdnaPosition: "185"
      cdsPosition: "105"
      proteinPosition: "35"
      aminoAcids: D
      codons: gaC/gaT
      existingVariation: rs533474523
      dbsnpId: "1"
      strand: "1"
      variantClass: SNV
      minimised: "1"
      symbolSource: HGNC
      hgncId: "20001"
      ensp: ENSP00000401598
      trembl: B4DEZ9
      uniparc: UPI00017A6F55
      genePheno: "1"
      domains:
        - id: PTHR10795
          source: hmmpanther
      gmaf: 0.0002
      afrMaf: 0.0002414
      amrMaf: 0
      easMaf: 0
      eurMaf: 0
      sasMaf: 0
      aaMaf: 0.001
      exacAdjMaf: 0
      exacAfrMaf: 0.00001679
      exacAmrMaf: 0
      exacEasMaf: 0.00007421
      exacFinMaf: 0
      exacNfeMaf: 0
      exacOthMaf: 0
      exacSasMaf: 0
      lofInfo: "EXON_START:55505431&DE_NOVO_DONOR_MES:-4.29805061924569&EXON_END:55505717&DE_NOVO_DONOR_MES_POS:-106&INTRON_START:55505718&INTRON_END:55509515&DE_NOVO_DONOR_POS:-105&MUTANT_DONOR_MES:8.16693067332728&DE_NOVO_DONOR_PROB:0.0706215314144107"
    - allele: T
      consequence: upstream_gene_variant
      impact: MODIFIER
      symbol: PCSK9
      gene: ENSG00000169174
      featureType: Transcript
      feature: ENST00000543384
      featureBiotype: protein_coding
      existingVariation: rs533474523
      dbsnpId: "1"
      distance: "280"
      strand: "1"
      variantClass: SNV
      minimised: "1"
      symbolSource: HGNC
      hgncId: "20001"
      ensp: ENSP00000441859
      trembl: F5GWF0
      uniparc: UPI000206501F
      genePheno: "1"
      gmaf: 0.0002
      afrMaf: 0.0002414
      amrMaf: 0
      easMaf: 0
      eurMaf: 0
      sasMaf: 0
      aaMaf: 0.001
      exacAdjMaf: 0
      exacAfrMaf: 0.00001679
      exacAmrMaf: 0
      exacEasMaf: 0.00007421
      exacFinMaf: 0
      exacNfeMaf: 0
      exacOthMaf: 0
      exacSasMaf: 0
    - allele: T
      consequence: regulatory_region_variant
      impact: MODIFIER
      featureType: RegulatoryFeature
      feature: ENSR00001037993
      featureBiotype: promoter
      existingVariation: rs533474523
      dbsnpId: "1"
      variantClass: SNV
      minimised: "1"
      gmaf: 0.0002
      afrMaf: 0.0002414
      amrMaf: 0
      easMaf: 0
      eurMaf: 0
      sasMaf: 0
      aaMaf: 0.001
      exacAdjMaf: 0
      exacAfrMaf: 0.00001679
      exacAmrMaf: 0
      exacEasMaf: 0.00007421
      exacFinMaf: 0
      exacNfeMaf: 0
      exacOthMaf: 0
      exacSasMaf: 0
  alleleCounts:
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        - population: afr
          counts:
            overall:
              an: 10794
            xx:
              an: 6732
            xy:
              an: 4062
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 27624
            xx:
              an: 15906
            xy:
              an: 11718
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 8924
            xx:
              an: 4230
            xy:
              an: 4694
        - population: eas
          counts:
            overall:
              an: 13610
            xx:
              an: 6736
            xy:
              an: 6874
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 72
        - population: eas_oea
          counts:
            overall:
              an: 10588
        - population: eas_kor
          counts:
            overall:
              an: 2950
        - population: fin
          counts:
            overall:
              an: 16742
            xx:
              an: 8614
            xy:
              an: 8128
        - population: nfe
          counts:
            overall:
              an: 77906
            xx:
              an: 35074
            xy:
              an: 42832
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 1378
        - population: nfe_est
          counts:
            overall:
              an: 214
        - population: nfe_nwe
          counts:
            overall:
              an: 37390
        - population: nfe_onf
          counts:
            overall:
              an: 22484
        - population: nfe_seu
          counts:
            overall:
              an: 4586
        - population: nfe_swe
          counts:
            overall:
              an: 11854
        - population: oth
          counts:
            overall:
              an: 4928
            xx:
              an: 2382
            xy:
              an: 2546
        - population: sas
          counts:
            overall:
              ac: 2
              an: 24344
              af: 0.0000821558
            xx:
              ac: 1
              an: 6138
              af: 0.00016292
            xy:
              ac: 1
              an: 18206
              af: 0.0000549269
          faf95: 0.00001459
          faf99: 0.00001408
      bySex:
        overall:
          ac: 2
          an: 184872
          af: 0.0000108183
        xx:
          ac: 1
          an: 85812
          af: 0.0000116534
        xy:
          ac: 1
          an: 99060
          af: 0.0000100949
      raw:
        ac: 16
        an: 250468
        af: 0.0000638804
      popmax: sas
      afPopmax: 0.0000821558
      acPopmax: 2
      anPopmax: 24344
      nhomaltPopmax: 0
    - cohort: controls
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 3926
            xx:
              an: 2244
            xy:
              an: 1682
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 13816
            xx:
              an: 8112
            xy:
              an: 5704
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 1660
            xx:
              an: 832
            xy:
              an: 828
        - population: eas
          counts:
            overall:
              an: 5850
            xx:
              an: 2986
            xy:
              an: 2864
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 44
        - population: eas_oea
          counts:
            overall:
              an: 4346
        - population: eas_kor
          counts:
            overall:
              an: 1460
        - population: fin
          counts:
            overall:
              an: 11828
            xx:
              an: 6044
            xy:
              an: 5784
        - population: nfe
          counts:
            overall:
              an: 28324
            xx:
              an: 12658
            xy:
              an: 15666
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 238
        - population: nfe_est
          counts:
            overall:
              an: 64
        - population: nfe_nwe
          counts:
            overall:
              an: 13108
        - population: nfe_onf
          counts:
            overall:
              an: 7430
        - population: nfe_seu
          counts:
            overall:
              an: 1640
        - population: nfe_swe
          counts:
            overall:
              an: 5844
        - population: oth
          counts:
            overall:
              an: 1528
            xx:
              an: 768
            xy:
              an: 760
        - population: sas
          counts:
            overall:
              ac: 2
              an: 12162
              af: 0.000164447
            xx:
              ac: 1
              an: 3368
              af: 0.000296912
            xy:
              ac: 1
              an: 8794
              af: 0.000113714
          faf95: 0.00001459
          faf99: 0.00001408
      bySex:
        overall:
          ac: 2
          an: 79094
          af: 0.0000252864
        xx:
          ac: 1
          an: 37012
          af: 0.0000270183
        xy:
          ac: 1
          an: 42082
          af: 0.0000237631
      raw:
        ac: 10
        an: 109012
        af: 0.000091733
      popmax: sas
      afPopmax: 0.000164447
      acPopmax: 2
      anPopmax: 12162
      nhomaltPopmax: 0
    - cohort: non_cancer
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 10026
            xx:
              an: 6204
            xy:
              an: 3822
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 27472
            xx:
              an: 15818
            xy:
              an: 11654
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 8660
            xx:
              an: 4086
            xy:
              an: 4574
        - population: eas
          counts:
            overall:
              an: 13232
            xx:
              an: 6522
            xy:
              an: 6710
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 54
        - population: eas_oea
          counts:
            overall:
              an: 10254
        - population: eas_kor
          counts:
            overall:
              an: 2924
        - population: fin
          counts:
            overall:
              an: 16734
            xx:
              an: 8608
            xy:
              an: 8126
        - population: nfe
          counts:
            overall:
              an: 72772
            xx:
              an: 32110
            xy:
              an: 40662
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 1320
        - population: nfe_est
          counts:
            overall:
              an: 152
        - population: nfe_nwe
          counts:
            overall:
              an: 35790
        - population: nfe_onf
          counts:
            overall:
              an: 19742
        - population: nfe_seu
          counts:
            overall:
              an: 4200
        - population: nfe_swe
          counts:
            overall:
              an: 11568
        - population: oth
          counts:
            overall:
              an: 4708
            xx:
              an: 2260
            xy:
              an: 2448
        - population: sas
          counts:
            overall:
              ac: 2
              an: 24310
              af: 0.0000822707
            xx:
              ac: 1
              an: 6120
              af: 0.000163399
            xy:
              ac: 1
              an: 18190
              af: 0.0000549753
          faf95: 0.00001459
          faf99: 0.00001408
      bySex:
        overall:
          ac: 2
          an: 177914
          af: 0.0000112414
        xx:
          ac: 1
          an: 81728
          af: 0.0000122357
        xy:
          ac: 1
          an: 96186
          af: 0.0000103965
      raw:
        ac: 14
        an: 236212
        af: 0.0000592688
      popmax: sas
      afPopmax: 0.0000822707
      acPopmax: 2
      anPopmax: 24310
      nhomaltPopmax: 0
    - cohort: non_neuro
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 10758
            xx:
              an: 6716
            xy:
              an: 4042
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 23562
            xx:
              an: 13904
            xy:
              an: 9658
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 5112
            xx:
              an: 2444
            xy:
              an: 2668
        - population: eas
          counts:
            overall:
              an: 10492
            xx:
              an: 5196
            xy:
              an: 5296
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 70
        - population: eas_oea
          counts:
            overall:
              an: 7474
        - population: eas_kor
          counts:
            overall:
              an: 2948
        - population: fin
          counts:
            overall:
              an: 14096
            xx:
              an: 7048
            xy:
              an: 7048
        - population: nfe
          counts:
            overall:
              an: 62434
            xx:
              an: 28834
            xy:
              an: 33600
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 320
        - population: nfe_est
          counts:
            overall:
              an: 188
        - population: nfe_nwe
          counts:
            overall:
              an: 30688
        - population: nfe_onf
          counts:
            overall:
              an: 19718
        - population: nfe_seu
          counts:
            overall:
              an: 4096
        - population: nfe_swe
          counts:
            overall:
              an: 7424
        - population: oth
          counts:
            overall:
              an: 3948
            xx:
              an: 1964
            xy:
              an: 1984
        - population: sas
          counts:
            overall:
              ac: 2
              an: 24338
              af: 0.000082176
            xx:
              ac: 1
              an: 6138
              af: 0.00016292
            xy:
              ac: 1
              an: 18200
              af: 0.0000549451
          faf95: 0.00001459
          faf99: 0.00001408
      bySex:
        overall:
          ac: 2
          an: 154740
          af: 0.0000129249
        xx:
          ac: 1
          an: 72244
          af: 0.000013842
        xy:
          ac: 1
          an: 82496
          af: 0.0000121218
      raw:
        ac: 13
        an: 207276
        af: 0.0000627183
      popmax: sas
      afPopmax: 0.000082176
      acPopmax: 2
      anPopmax: 24338
      nhomaltPopmax: 0
    - cohort: non_topmed
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 9346
            xx:
              an: 5744
            xy:
              an: 3602
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 27548
            xx:
              an: 15860
            xy:
              an: 11688
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 8850
            xx:
              an: 4190
            xy:
              an: 4660
        - population: eas
          counts:
            overall:
              an: 13606
            xx:
              an: 6736
            xy:
              an: 6870
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 72
        - population: eas_oea
          counts:
            overall:
              an: 10584
        - population: eas_kor
          counts:
            overall:
              an: 2950
        - population: fin
          counts:
            overall:
              an: 16740
            xx:
              an: 8612
            xy:
              an: 8128
        - population: nfe
          counts:
            overall:
              an: 76176
            xx:
              an: 33988
            xy:
              an: 42188
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 1372
        - population: nfe_est
          counts:
            overall:
              an: 210
        - population: nfe_nwe
          counts:
            overall:
              an: 36332
        - population: nfe_onf
          counts:
            overall:
              an: 21892
        - population: nfe_seu
          counts:
            overall:
              an: 4550
        - population: nfe_swe
          counts:
            overall:
              an: 11820
        - population: oth
          counts:
            overall:
              an: 4860
            xx:
              an: 2340
            xy:
              an: 2520
        - population: sas
          counts:
            overall:
              ac: 2
              an: 24344
              af: 0.0000821558
            xx:
              ac: 1
              an: 6138
              af: 0.00016292
            xy:
              ac: 1
              an: 18206
              af: 0.0000549269
          faf95: 0.00001459
          faf99: 0.00001408
      bySex:
        overall:
          ac: 2
          an: 181470
          af: 0.0000110211
        xx:
          ac: 1
          an: 83608
          af: 0.0000119606
        xy:
          ac: 1
          an: 97862
          af: 0.0000102185
      raw:
        ac: 15
        an: 243924
        af: 0.0000614946
      popmax: sas
      afPopmax: 0.0000821558
      acPopmax: 2
      anPopmax: 24344
      nhomaltPopmax: 0
  rfInfo:
    rfTpProbability: 0.160052
  variantInfo:
    variantType: snv
    alleleType: snv
    nAltAlleles: 1
  qualityInfo:
    fs: 0
    inbreedingCoeff: -0.0069
    mq: 60
    mqRankSum: -0.537
    qd: 8.06
    readPosRankSum: -0.317
    baseQRankSum: -1.589
    clippingRankSum: -0.572
    sor: 0.655
    dp: 9465840
    vqslod: 0.1
    vqsrCulprit: MQ
    pabMax: 1
  ageInfo:
    ageHistHomNSmaller: 0
    ageHistHomNLarger: 0
    ageHistHetNSmaller: 0
    ageHistHetNLarger: 0
  depthInfo:
    dpHistAllNLarger: 13666
    dpHistAltNLarger: 1
- chrom: "1"
  pos: 55516888
  refAllele: G
  altAllele: A
  vep:
    - allele: A
      consequence: intron_variant
      impact: MODIFIER
      symbol: PCSK9
      gene: ENSG00000169174
      featureType: Transcript
      feature: ENST00000302118
      featureBiotype: protein_coding
      intron: 3/11
      hgvsc: "ENST00000302118.5:c.524-1063G>A"
      existingVariation: rs778104784
      dbsnpId: "1"
      strand: "1"
      variantClass: SNV
      minimised: "1"
      symbolSource: HGNC
      hgncId: "20001"
      canonical: true
      ccds: CCDS603.1
      ensp: ENSP00000303208
      swissprot: Q8NBP7
      uniparc: UPI00001615E1
      genePheno: "1"
    - allele: A
      consequence: missense_variant
      impact: MODERATE
      symbol: PCSK9
      gene: ENSG00000169174
      featureType: Transcript
      feature: ENST00000452118
      featureBiotype: protein_coding
      exon: 4/6
      hgvsc: "ENST00000452118.2:c.547G>A"
      hgvsp: "ENSP00000401598.2:p.Gly183Ser"
      cdnaPosition: "627"
      cdsPosition: "547"
      proteinPosition: "183"
      aminoAcids: G/S
      codons: Ggc/Agc
      existingVariation: rs778104784
      dbsnpId: "1"
      strand: "1"
      variantClass: SNV
      minimised: "1"
      symbolSource: HGNC
      hgncId: "20001"
      ensp: ENSP00000401598
      trembl: B4DEZ9
      uniparc: UPI00017A6F55
      genePheno: "1"
      sift:
        prediction: deleterious_low_confidence
      polyphen:
        prediction: possibly_damaging
        score: 0.86
    - allele: A
      consequence: non_coding_transcript_exon_variant&non_coding_transcript_variant
      impact: MODIFIER
      symbol: PCSK9
      gene: ENSG00000169174
      featureType: Transcript
      feature: ENST00000490692
      featureBiotype: processed_transcript
      exon: 1/8
      hgvsc: "ENST00000490692.1:n.282G>A"
      cdnaPosition: "282"
      existingVariation: rs778104784
      dbsnpId: "1"
      strand: "1"
      variantClass: SNV
      minimised: "1"
      symbolSource: HGNC
      hgncId: "20001"
      genePheno: "1"
    - allele: A
      consequence: intron_variant
      impact: MODIFIER
      symbol: PCSK9
      gene: ENSG00000169174
      featureType: Transcript
      feature: ENST00000543384
      featureBiotype: protein_coding
      intron: 1/9
      hgvsc: "ENST00000543384.1:c.-77-1063G>A"
      existingVariation: rs778104784
      dbsnpId: "1"
      strand: "1"
      variantClass: SNV
      minimised: "1"
      symbolSource: HGNC
      hgncId: "20001"
      ensp: ENSP00000441859
      trembl: F5GWF0
      uniparc: UPI000206501F
      genePheno: "1"
  alleleCounts:
    - byPopulation:
        - population: afr
          counts:
            overall:
              an: 6082
            xx:
              an: 3486
            xy:
              an: 2596
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 24326
            xx:
              an: 14030
            xy:
              an: 10296
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 8088
            xx:
              an: 3812
            xy:
              an: 4276
        - population: eas
          counts:
            overall:
              an: 10426
            xx:
              an: 5084
            xy:
              an: 5342
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 10
        - population: eas_oea
          counts:
            overall:
              an: 8548
        - population: eas_kor
          counts:
            overall:
              an: 1868
        - population: fin
          counts:
            overall:
              an: 5380
            xx:
              an: 2762
            xy:
              an: 2618
        - population: nfe
          counts:
            overall:
              an: 47556
            xx:
              an: 21402
            xy:
              an: 26154
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 248
        - population: nfe_est
          counts:
            overall:
              an: 130
        - population: nfe_nwe
          counts:
            overall:
              an: 29854
        - population: nfe_onf
          counts:
            overall:
              an: 14498
        - population: nfe_seu
          counts:
            overall:
              an: 1292
        - population: nfe_swe
          counts:
            overall:
              an: 1534
        - population: oth
          counts:
            overall:
              an: 3988
            xx:
              an: 1924
            xy:
              an: 2064
        - population: sas
          counts:
            overall:
              ac: 8
              an: 22384
              af: 0.000357398
            xx:
              ac: 3
              an: 5516
              af: 0.000543872
            xy:
              ac: 5
              an: 16868
              af: 0.000296419
          faf95: 0.00017773
          faf99: 0.00017709
      bySex:
        overall:
          ac: 8
          an: 128230
          af: 0.0000623879
        xx:
          ac: 3
          an: 58016
          af: 0.0000517099
        xy:
          ac: 5
          an: 70214
          af: 0.0000712109
      raw:
        ac: 10
        an: 142752
        af: 0.0000700516
      popmax: sas
      afPopmax: 0.000357398
      acPopmax: 8
      anPopmax: 22384
      nhomaltPopmax: 0
    - cohort: controls
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 2368
            xx:
              an: 1344
            xy:
              an: 1024
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 12120
            xx:
              an: 7112
            xy:
              an: 5008
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 1454
            xx:
              an: 710
            xy:
              an: 744
        - population: eas
          counts:
            overall:
              an: 3994
            xx:
              an: 2008
            xy:
              an: 1986
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts:
            overall:
              an: 3066
        - population: eas_kor
          counts:
            overall:
              an: 928
        - population: fin
          counts:
            overall:
              an: 1506
            xx:
              an: 668
            xy:
              an: 838
        - population: nfe
          counts:
            overall:
              an: 18962
            xx:
              an: 8658
            xy:
              an: 10304
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 74
        - population: nfe_est
          counts:
            overall:
              an: 58
        - population: nfe_nwe
          counts:
            overall:
              an: 12206
        - population: nfe_onf
          counts:
            overall:
              an: 5932
        - population: nfe_seu
          counts:
            overall:
              an: 318
        - population: nfe_swe
          counts:
            overall:
              an: 374
        - population: oth
          counts:
            overall:
              an: 1272
            xx:
              an: 640
            xy:
              an: 632
        - population: sas
          counts:
            overall:
              ac: 4
              an: 11062
              af: 0.000361598
            xx:
              ac: 1
              an: 2994
              af: 0.000334001
            xy:
              ac: 3
              an: 8068
              af: 0.000371839
          faf95: 0.00017773
          faf99: 0.00017709
      bySex:
        overall:
          ac: 4
          an: 52738
          af: 0.0000758466
        xx:
          ac: 1
          an: 24134
          af: 0.0000414353
        xy:
          ac: 3
          an: 28604
          af: 0.00010488
      raw:
        ac: 4
        an: 57802
        af: 0.0000692018
      popmax: sas
      afPopmax: 0.000361598
      acPopmax: 4
      anPopmax: 11062
      nhomaltPopmax: 0
    - cohort: non_cancer
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 6078
            xx:
              an: 3486
            xy:
              an: 2592
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 24324
            xx:
              an: 14030
            xy:
              an: 10294
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 8086
            xx:
              an: 3812
            xy:
              an: 4274
        - population: eas
          counts:
            overall:
              an: 10420
            xx:
              an: 5084
            xy:
              an: 5336
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 10
        - population: eas_oea
          counts:
            overall:
              an: 8542
        - population: eas_kor
          counts:
            overall:
              an: 1868
        - population: fin
          counts:
            overall:
              an: 5380
            xx:
              an: 2762
            xy:
              an: 2618
        - population: nfe
          counts:
            overall:
              an: 47510
            xx:
              an: 21382
            xy:
              an: 26128
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 248
        - population: nfe_est
          counts:
            overall:
              an: 128
        - population: nfe_nwe
          counts:
            overall:
              an: 29840
        - population: nfe_onf
          counts:
            overall:
              an: 14470
        - population: nfe_seu
          counts:
            overall:
              an: 1292
        - population: nfe_swe
          counts:
            overall:
              an: 1532
        - population: oth
          counts:
            overall:
              an: 3988
            xx:
              an: 1924
            xy:
              an: 2064
        - population: sas
          counts:
            overall:
              ac: 8
              an: 22384
              af: 0.000357398
            xx:
              ac: 3
              an: 5516
              af: 0.000543872
            xy:
              ac: 5
              an: 16868
              af: 0.000296419
          faf95: 0.00017773
          faf99: 0.00017709
      bySex:
        overall:
          ac: 8
          an: 128170
          af: 0.0000624171
        xx:
          ac: 3
          an: 57996
          af: 0.0000517277
        xy:
          ac: 5
          an: 70174
          af: 0.0000712515
      raw:
        ac: 9
        an: 139372
        af: 0.0000645754
      popmax: sas
      afPopmax: 0.000357398
      acPopmax: 8
      anPopmax: 22384
      nhomaltPopmax: 0
    - cohort: non_neuro
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 6050
            xx:
              an: 3474
            xy:
              an: 2576
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 20320
            xx:
              an: 12050
            xy:
              an: 8270
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 4460
            xx:
              an: 2092
            xy:
              an: 2368
        - population: eas
          counts:
            overall:
              an: 7920
            xx:
              an: 3824
            xy:
              an: 4096
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 8
        - population: eas_oea
          counts:
            overall:
              an: 6046
        - population: eas_kor
          counts:
            overall:
              an: 1866
        - population: fin
          counts:
            overall:
              an: 3506
            xx:
              an: 1604
            xy:
              an: 1902
        - population: nfe
          counts:
            overall:
              an: 42406
            xx:
              an: 19602
            xy:
              an: 22804
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 224
        - population: nfe_est
          counts:
            overall:
              an: 118
        - population: nfe_nwe
          counts:
            overall:
              an: 26018
        - population: nfe_onf
          counts:
            overall:
              an: 13456
        - population: nfe_seu
          counts:
            overall:
              an: 1110
        - population: nfe_swe
          counts:
            overall:
              an: 1480
        - population: oth
          counts:
            overall:
              an: 3284
            xx:
              an: 1628
            xy:
              an: 1656
        - population: sas
          counts:
            overall:
              ac: 8
              an: 22382
              af: 0.00035743
            xx:
              ac: 3
              an: 5516
              af: 0.000543872
            xy:
              ac: 5
              an: 16866
              af: 0.000296454
          faf95: 0.00017773
          faf99: 0.00017709
      bySex:
        overall:
          ac: 8
          an: 110328
          af: 0.0000725111
        xx:
          ac: 3
          an: 49790
          af: 0.0000602531
        xy:
          ac: 5
          an: 60538
          af: 0.0000825928
      raw:
        ac: 10
        an: 121616
        af: 0.000082226
      popmax: sas
      afPopmax: 0.00035743
      acPopmax: 8
      anPopmax: 22382
      nhomaltPopmax: 0
    - cohort: non_topmed
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 5912
            xx:
              an: 3372
            xy:
              an: 2540
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 24272
            xx:
              an: 14000
            xy:
              an: 10272
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 8048
            xx:
              an: 3794
            xy:
              an: 4254
        - population: eas
          counts:
            overall:
              an: 10422
            xx:
              an: 5084
            xy:
              an: 5338
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 10
        - population: eas_oea
          counts:
            overall:
              an: 8544
        - population: eas_kor
          counts:
            overall:
              an: 1868
        - population: fin
          counts:
            overall:
              an: 5378
            xx:
              an: 2760
            xy:
              an: 2618
        - population: nfe
          counts:
            overall:
              an: 46514
            xx:
              an: 20834
            xy:
              an: 25680
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 248
        - population: nfe_est
          counts:
            overall:
              an: 126
        - population: nfe_nwe
          counts:
            overall:
              an: 29112
        - population: nfe_onf
          counts:
            overall:
              an: 14202
        - population: nfe_seu
          counts:
            overall:
              an: 1292
        - population: nfe_swe
          counts:
            overall:
              an: 1534
        - population: oth
          counts:
            overall:
              an: 3938
            xx:
              an: 1898
            xy:
              an: 2040
        - population: sas
          counts:
            overall:
              ac: 8
              an: 22384
              af: 0.000357398
            xx:
              ac: 3
              an: 5516
              af: 0.000543872
            xy:
              ac: 5
              an: 16868
              af: 0.000296419
          faf95: 0.00017773
          faf99: 0.00017709
      bySex:
        overall:
          ac: 8
          an: 126868
          af: 0.0000630577
        xx:
          ac: 3
          an: 57258
          af: 0.0000523944
        xy:
          ac: 5
          an: 69610
          af: 0.0000718288
      raw:
        ac: 10
        an: 140614
        af: 0.0000711167
      popmax: sas
      afPopmax: 0.000357398
      acPopmax: 8
      anPopmax: 22384
      nhomaltPopmax: 0
  rfInfo:
    rfTpProbability: 0.832565
    rfPositiveLabel: true
    rfLabel: TP
    rfTrain: true
  variantInfo:
    variantType: mixed
    alleleType: snv
    nAltAlleles: 3
    wasMixed: true
  qualityInfo:
    fs: 0.568
    inbreedingCoeff: 0.0346
    mq: 59.75
    mqRankSum: 0.459
    qd: 15.76
    readPosRankSum: 0
    vqsrPositiveTrainSite: true
    baseQRankSum: 1.45
    clippingRankSum: 0.137
    sor: 0.767
    dp: 3701481
    vqslod: 6.1
    vqsrCulprit: FS
    pabMax: 1
  ageInfo:
    ageHistHomNSmaller: 0
    ageHistHomNLarger: 0
    ageHistHetNSmaller: 0
    ageHistHetNLarger: 0
  depthInfo:
    dpHistAllNLarger: 26
    dpHistAltNLarger: 0
- chrom: "1"
  pos: 55516888
  refAllele: G
  altAllele: GA
  vep:
    - allele: A
      consequence: intron_variant
      impact: MODIFIER
      symbol: PCSK9
      gene: ENSG00000169174
      featureType: Transcript
      feature: ENST00000302118
      featureBiotype: protein_coding
      intron: 3/11
      hgvsc: "ENST00000302118.5:c.524-1063_524-1062insA"
      existingVariation: rs527413419
      dbsnpId: "1"
      strand: "1"
      variantClass: insertion
      minimised: "1"
      symbolSource: HGNC
      hgncId: "20001"
      canonical: true
      ccds: CCDS603.1
      ensp: ENSP00000303208
      swissprot: Q8NBP7
      uniparc: UPI00001615E1
      genePheno: "1"
      gmaf: 0.0032
      amrMaf: 0.0113
      easMaf: 0.0014
      eurMaf: 0
      sasMaf: 0
      aaMaf: 0
    - allele: A
      consequence: frameshift_variant
      impact: HIGH
      symbol: PCSK9
      gene: ENSG00000169174
      featureType: Transcript
      feature: ENST00000452118
      featureBiotype: protein_coding
      exon: 4/6
      hgvsc: "ENST00000452118.2:c.547_548insA"
      hgvsp: "ENSP00000401598.2:p.Gly183GlufsTer23"
      cdnaPosition: 627-628
      cdsPosition: 547-548
      proteinPosition: "183"
      aminoAcids: G/EX
      codons: ggc/gAgc
      existingVariation: rs527413419
      dbsnpId: "1"
      strand: "1"
      variantClass: insertion
      minimised: "1"
      symbolSource: HGNC
      hgncId: "20001"
      ensp: ENSP00000401598
      trembl: B4DEZ9
      uniparc: UPI00017A6F55
      genePheno: "1"
      gmaf: 0.0032
      amrMaf: 0.0113
      easMaf: 0.0014
      eurMaf: 0
      sasMaf: 0
      aaMaf: 0
      lof: HC
      lofInfo: "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
      featureType: Transcript
      feature: ENST00000490692
      featureBiotype: processed_transcript
      exon: 1/8
      hgvsc: "ENST00000490692.1:n.282_283insA"
      cdnaPosition: 282-283
      existingVariation: rs527413419
      dbsnpId: "1"
      strand: "1"
      variantClass: insertion
      minimised: "1"
      symbolSource: HGNC
      hgncId: "20001"
      genePheno: "1"
      gmaf: 0.0032
      amrMaf: 0.0113
      easMaf: 0.0014
      eurMaf: 0
      sasMaf: 0
      aaMaf: 0
    - allele: A
      consequence: intron_variant
      impact: MODIFIER
      symbol: PCSK9
      gene: ENSG00000169174
      featureType: Transcript
      feature: ENST00000543384
      featureBiotype: protein_coding
      intron: 1/9
      hgvsc: "ENST00000543384.1:c.-77-1063_-77-1062insA"
      existingVariation: rs527413419
      dbsnpId: "1"
      strand: "1"
      variantClass: insertion
      minimised: "1"
      symbolSource: HGNC
      hgncId: "20001"
      ensp: ENSP00000441859
      trembl: F5GWF0
      uniparc: UPI000206501F
      genePheno: "1"
      gmaf: 0.0032
      amrMaf: 0.0113
      easMaf: 0.0014
      eurMaf: 0
      sasMaf: 0
      aaMaf: 0
  alleleCounts:
    - byPopulation:
        - population: afr
          counts:
            overall:
              ac: 97
              an: 6082
              nhomalt: 2
              af: 0.0159487
            xx:
              ac: 66
              an: 3486
              nhomalt: 1
              af: 0.0189329
            xy:
              ac: 31
              an: 2596
              nhomalt: 1
              af: 0.0119414
          faf95: 0.0133815
          faf99: 0.0133811
        - population: amr
          counts:
            overall:
              ac: 18
              an: 24326
              af: 0.000739949
            xx:
              ac: 11
              an: 14030
              af: 0.000784034
            xy:
              ac: 7
              an: 10296
              af: 0.000679876
          faf95: 0.0004775
          faf99: 0.00047812
        - population: asj
          counts:
            overall:
              an: 8088
            xx:
              an: 3812
            xy:
              an: 4276
        - population: eas
          counts:
            overall:
              an: 10426
            xx:
              an: 5084
            xy:
              an: 5342
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 10
        - population: eas_oea
          counts:
            overall:
              an: 8548
        - population: eas_kor
          counts:
            overall:
              an: 1868
        - population: fin
          counts:
            overall:
              an: 5380
            xx:
              an: 2762
            xy:
              an: 2618
        - population: nfe
          counts:
            overall:
              ac: 4
              an: 47556
              af: 0.0000841114
            xx:
              ac: 2
              an: 21402
              af: 0.0000934492
            xy:
              ac: 2
              an: 26154
              af: 0.0000764701
          faf95: 0.00002861
          faf99: 0.00002821
        - population: nfe_bgr
          counts:
            overall:
              an: 248
        - population: nfe_est
          counts:
            overall:
              an: 130
        - population: nfe_nwe
          counts:
            overall:
              ac: 4
              an: 29854
              af: 0.000133985
        - population: nfe_onf
          counts:
            overall:
              an: 14498
        - population: nfe_seu
          counts:
            overall:
              an: 1292
        - population: nfe_swe
          counts:
            overall:
              an: 1534
        - population: oth
          counts:
            overall:
              ac: 2
              an: 3988
              af: 0.000501505
            xx:
              ac: 1
              an: 1924
              af: 0.000519751
            xy:
              ac: 1
              an: 2064
              af: 0.000484496
        - population: sas
          counts:
            overall:
              an: 22384
            xx:
              an: 5516
            xy:
              an: 16868
          faf95: 0
          faf99: 0
      bySex:
        overall:
          ac: 121
          an: 128230
          nhomalt: 2
          af: 0.000943617
        xx:
          ac: 80
          an: 58016
          nhomalt: 1
          af: 0.00137893
        xy:
          ac: 41
          an: 70214
          nhomalt: 1
          af: 0.000583929
      raw:
        ac: 125
        an: 142752
        nhomalt: 3
        af: 0.000875644
      popmax: afr
      afPopmax: 0.0159487
      acPopmax: 97
      anPopmax: 6082
      nhomaltPopmax: 2
    - cohort: controls
      byPopulation:
        - population: afr
          counts:
            overall:
              ac: 50
              an: 2368
              nhomalt: 1
              af: 0.0211149
            xx:
              ac: 31
              an: 1344
              af: 0.0230655
            xy:
              ac: 19
              an: 1024
              nhomalt: 1
              af: 0.0185547
          faf95: 0.0133815
          faf99: 0.0133811
        - population: amr
          counts:
            overall:
              ac: 12
              an: 12120
              af: 0.000990099
            xx:
              ac: 8
              an: 7112
              af: 0.00112486
            xy:
              ac: 4
              an: 5008
              af: 0.000798722
          faf95: 0.0004775
          faf99: 0.00047812
        - population: asj
          counts:
            overall:
              an: 1454
            xx:
              an: 710
            xy:
              an: 744
        - population: eas
          counts:
            overall:
              an: 3994
            xx:
              an: 2008
            xy:
              an: 1986
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts:
            overall:
              an: 3066
        - population: eas_kor
          counts:
            overall:
              an: 928
        - population: fin
          counts:
            overall:
              an: 1506
            xx:
              an: 668
            xy:
              an: 838
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 18962
              af: 0.0000527371
            xx:
              ac: 1
              an: 8658
              af: 0.0001155
            xy:
              an: 10304
          faf95: 0.00002861
          faf99: 0.00002821
        - population: nfe_bgr
          counts:
            overall:
              an: 74
        - population: nfe_est
          counts:
            overall:
              an: 58
        - population: nfe_nwe
          counts:
            overall:
              ac: 1
              an: 12206
              af: 0.0000819269
        - population: nfe_onf
          counts:
            overall:
              an: 5932
        - population: nfe_seu
          counts:
            overall:
              an: 318
        - population: nfe_swe
          counts:
            overall:
              an: 374
        - population: oth
          counts:
            overall:
              an: 1272
            xx:
              an: 640
            xy:
              an: 632
        - population: sas
          counts:
            overall:
              an: 11062
            xx:
              an: 2994
            xy:
              an: 8068
          faf95: 0
          faf99: 0
      bySex:
        overall:
          ac: 63
          an: 52738
          nhomalt: 1
          af: 0.00119458
        xx:
          ac: 40
          an: 24134
          af: 0.00165741
        xy:
          ac: 23
          an: 28604
          nhomalt: 1
          af: 0.000804083
      raw:
        ac: 64
        an: 57802
        nhomalt: 1
        af: 0.00110723
      popmax: afr
      afPopmax: 0.0211149
      acPopmax: 50
      anPopmax: 2368
      nhomaltPopmax: 1
    - cohort: non_cancer
      byPopulation:
        - population: afr
          counts:
            overall:
              ac: 97
              an: 6078
              nhomalt: 2
              af: 0.0159592
            xx:
              ac: 66
              an: 3486
              nhomalt: 1
              af: 0.0189329
            xy:
              ac: 31
              an: 2592
              nhomalt: 1
              af: 0.0119599
          faf95: 0.0133815
          faf99: 0.0133811
        - population: amr
          counts:
            overall:
              ac: 18
              an: 24324
              af: 0.00074001
            xx:
              ac: 11
              an: 14030
              af: 0.000784034
            xy:
              ac: 7
              an: 10294
              af: 0.000680008
          faf95: 0.0004775
          faf99: 0.00047812
        - population: asj
          counts:
            overall:
              an: 8086
            xx:
              an: 3812
            xy:
              an: 4274
        - population: eas
          counts:
            overall:
              an: 10420
            xx:
              an: 5084
            xy:
              an: 5336
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 10
        - population: eas_oea
          counts:
            overall:
              an: 8542
        - population: eas_kor
          counts:
            overall:
              an: 1868
        - population: fin
          counts:
            overall:
              an: 5380
            xx:
              an: 2762
            xy:
              an: 2618
        - population: nfe
          counts:
            overall:
              ac: 4
              an: 47510
              af: 0.0000841928
            xx:
              ac: 2
              an: 21382
              af: 0.0000935366
            xy:
              ac: 2
              an: 26128
              af: 0.0000765462
          faf95: 0.00002861
          faf99: 0.00002821
        - population: nfe_bgr
          counts:
            overall:
              an: 248
        - population: nfe_est
          counts:
            overall:
              an: 128
        - population: nfe_nwe
          counts:
            overall:
              ac: 4
              an: 29840
              af: 0.000134048
        - population: nfe_onf
          counts:
            overall:
              an: 14470
        - population: nfe_seu
          counts:
            overall:
              an: 1292
        - population: nfe_swe
          counts:
            overall:
              an: 1532
        - population: oth
          counts:
            overall:
              ac: 2
              an: 3988
              af: 0.000501505
            xx:
              ac: 1
              an: 1924
              af: 0.000519751
            xy:
              ac: 1
              an: 2064
              af: 0.000484496
        - population: sas
          counts:
            overall:
              an: 22384
            xx:
              an: 5516
            xy:
              an: 16868
          faf95: 0
          faf99: 0
      bySex:
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          ac: 121
          an: 128170
          nhomalt: 2
          af: 0.000944059
        xx:
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          an: 57996
          nhomalt: 1
          af: 0.00137941
        xy:
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          an: 70174
          nhomalt: 1
          af: 0.000584262
      raw:
        ac: 123
        an: 139372
        nhomalt: 2
        af: 0.00088253
      popmax: afr
      afPopmax: 0.0159592
      acPopmax: 97
      anPopmax: 6078
      nhomaltPopmax: 2
    - cohort: non_neuro
      byPopulation:
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          counts:
            overall:
              ac: 97
              an: 6050
              nhomalt: 2
              af: 0.0160331
            xx:
              ac: 66
              an: 3474
              nhomalt: 1
              af: 0.0189983
            xy:
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              an: 2576
              nhomalt: 1
              af: 0.0120342
          faf95: 0.0133815
          faf99: 0.0133811
        - population: amr
          counts:
            overall:
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              an: 20320
              af: 0.000639764
            xx:
              ac: 8
              an: 12050
              af: 0.0006639
            xy:
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              an: 8270
              af: 0.000604595
          faf95: 0.0004775
          faf99: 0.00047812
        - population: asj
          counts:
            overall:
              an: 4460
            xx:
              an: 2092
            xy:
              an: 2368
        - population: eas
          counts:
            overall:
              an: 7920
            xx:
              an: 3824
            xy:
              an: 4096
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 8
        - population: eas_oea
          counts:
            overall:
              an: 6046
        - population: eas_kor
          counts:
            overall:
              an: 1866
        - population: fin
          counts:
            overall:
              an: 3506
            xx:
              an: 1604
            xy:
              an: 1902
        - population: nfe
          counts:
            overall:
              ac: 2
              an: 42406
              af: 0.0000471631
            xx:
              ac: 1
              an: 19602
              af: 0.0000510152
            xy:
              ac: 1
              an: 22804
              af: 0.000043852
          faf95: 0.00002861
          faf99: 0.00002821
        - population: nfe_bgr
          counts:
            overall:
              an: 224
        - population: nfe_est
          counts:
            overall:
              an: 118
        - population: nfe_nwe
          counts:
            overall:
              ac: 2
              an: 26018
              af: 0.0000768699
        - population: nfe_onf
          counts:
            overall:
              an: 13456
        - population: nfe_seu
          counts:
            overall:
              an: 1110
        - population: nfe_swe
          counts:
            overall:
              an: 1480
        - population: oth
          counts:
            overall:
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              an: 3284
              af: 0.000609013
            xx:
              ac: 1
              an: 1628
              af: 0.000614251
            xy:
              ac: 1
              an: 1656
              af: 0.000603865
        - population: sas
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            overall:
              an: 22382
            xx:
              an: 5516
            xy:
              an: 16866
          faf95: 0
          faf99: 0
      bySex:
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          an: 110328
          nhomalt: 2
          af: 0.00103328
        xx:
          ac: 76
          an: 49790
          nhomalt: 1
          af: 0.00152641
        xy:
          ac: 38
          an: 60538
          nhomalt: 1
          af: 0.000627705
      raw:
        ac: 118
        an: 121616
        nhomalt: 3
        af: 0.000970267
      popmax: afr
      afPopmax: 0.0160331
      acPopmax: 97
      anPopmax: 6050
      nhomaltPopmax: 2
    - cohort: non_topmed
      byPopulation:
        - population: afr
          counts:
            overall:
              ac: 90
              an: 5912
              nhomalt: 2
              af: 0.0152233
            xx:
              ac: 61
              an: 3372
              nhomalt: 1
              af: 0.0180902
            xy:
              ac: 29
              an: 2540
              nhomalt: 1
              af: 0.0114173
          faf95: 0.0133815
          faf99: 0.0133811
        - population: amr
          counts:
            overall:
              ac: 18
              an: 24272
              af: 0.000741595
            xx:
              ac: 11
              an: 14000
              af: 0.000785714
            xy:
              ac: 7
              an: 10272
              af: 0.000681464
          faf95: 0.0004775
          faf99: 0.00047812
        - population: asj
          counts:
            overall:
              an: 8048
            xx:
              an: 3794
            xy:
              an: 4254
        - population: eas
          counts:
            overall:
              an: 10422
            xx:
              an: 5084
            xy:
              an: 5338
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 10
        - population: eas_oea
          counts:
            overall:
              an: 8544
        - population: eas_kor
          counts:
            overall:
              an: 1868
        - population: fin
          counts:
            overall:
              an: 5378
            xx:
              an: 2760
            xy:
              an: 2618
        - population: nfe
          counts:
            overall:
              ac: 4
              an: 46514
              af: 0.0000859956
            xx:
              ac: 2
              an: 20834
              af: 0.0000959969
            xy:
              ac: 2
              an: 25680
              af: 0.0000778816
          faf95: 0.00002861
          faf99: 0.00002821
        - population: nfe_bgr
          counts:
            overall:
              an: 248
        - population: nfe_est
          counts:
            overall:
              an: 126
        - population: nfe_nwe
          counts:
            overall:
              ac: 4
              an: 29112
              af: 0.0001374
        - population: nfe_onf
          counts:
            overall:
              an: 14202
        - population: nfe_seu
          counts:
            overall:
              an: 1292
        - population: nfe_swe
          counts:
            overall:
              an: 1534
        - population: oth
          counts:
            overall:
              ac: 2
              an: 3938
              af: 0.000507872
            xx:
              ac: 1
              an: 1898
              af: 0.00052687
            xy:
              ac: 1
              an: 2040
              af: 0.000490196
        - population: sas
          counts:
            overall:
              an: 22384
            xx:
              an: 5516
            xy:
              an: 16868
          faf95: 0
          faf99: 0
      bySex:
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          an: 126868
          nhomalt: 2
          af: 0.000898572
        xx:
          ac: 75
          an: 57258
          nhomalt: 1
          af: 0.00130986
        xy:
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          an: 69610
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          af: 0.000560264
      raw:
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        an: 140614
        nhomalt: 3
        af: 0.000839177
      popmax: afr
      afPopmax: 0.0152233
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      anPopmax: 5912
      nhomaltPopmax: 2
  rfInfo:
    rfTpProbability: 0.831697
    rfPositiveLabel: true
    rfLabel: TP
    rfTrain: true
  variantInfo:
    variantType: mixed
    alleleType: ins
    nAltAlleles: 3
    wasMixed: true
  qualityInfo:
    fs: 0.568
    inbreedingCoeff: 0.0346
    mq: 59.75
    mqRankSum: 0.459
    qd: 15.76
    readPosRankSum: 0
    vqsrPositiveTrainSite: true
    baseQRankSum: 1.45
    clippingRankSum: 0.137
    sor: 0.767
    dp: 3701481
    vqslod: 6.1
    vqsrCulprit: FS
    pabMax: 1
  ageInfo:
    ageHistHomNSmaller: 0
    ageHistHomNLarger: 0
    ageHistHetNSmaller: 9
    ageHistHetNLarger: 1
  depthInfo:
    dpHistAllNLarger: 26
    dpHistAltNLarger: 0
- chrom: X
  pos: 69902557
  refAllele: G
  altAllele: T
  vep:
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      consequence: missense_variant
      impact: MODERATE
      symbol: TEX11
      gene: ENSG00000120498
      featureType: Transcript
      feature: ENST00000344304
      featureBiotype: protein_coding
      exon: 13/29
      hgvsc: "ENST00000344304.3:c.1168C>A"
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      cdsPosition: "1168"
      proteinPosition: "390"
      aminoAcids: L/I
      codons: Ctt/Att
      dbsnpId: "1"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: HGNC
      hgncId: "11733"
      ccds: CCDS35323.1
      ensp: ENSP00000340995
      swissprot: Q8IYF3
      uniparc: UPI000013CA89
      genePheno: "1"
      sift:
        prediction: tolerated
        score: 0.17
      polyphen:
        prediction: benign
        score: 0.105
      domains:
        - id: seg
          source: Low_complexity_(Seg)
        - id: PTHR22904
          source: hmmpanther
        - id: PTHR22904
          source: hmmpanther
        - id: PF08631
          source: Pfam_domain
    - allele: T
      consequence: missense_variant
      impact: MODERATE
      symbol: TEX11
      gene: ENSG00000120498
      featureType: Transcript
      feature: ENST00000374320
      featureBiotype: protein_coding
      exon: 3/19
      hgvsc: "ENST00000374320.2:c.193C>A"
      hgvsp: "ENSP00000363440.2:p.Leu65Ile"
      cdnaPosition: "415"
      cdsPosition: "193"
      proteinPosition: "65"
      aminoAcids: L/I
      codons: Ctt/Att
      dbsnpId: "1"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: HGNC
      hgncId: "11733"
      ensp: ENSP00000363440
      swissprot: Q8IYF3
      uniparc: UPI00004A2D6C
      genePheno: "1"
      sift:
        prediction: tolerated
        score: 0.12
      polyphen:
        prediction: benign
        score: 0.105
      domains:
        - id: seg
          source: Low_complexity_(Seg)
        - id: PTHR22904
          source: hmmpanther
        - id: PTHR22904
          source: hmmpanther
        - id: PF08631
          source: Pfam_domain
    - allele: T
      consequence: missense_variant
      impact: MODERATE
      symbol: TEX11
      gene: ENSG00000120498
      featureType: Transcript
      feature: ENST00000374333
      featureBiotype: protein_coding
      exon: 14/30
      hgvsc: "ENST00000374333.2:c.1123C>A"
      hgvsp: "ENSP00000363453.2:p.Leu375Ile"
      cdnaPosition: "1222"
      cdsPosition: "1123"
      proteinPosition: "375"
      aminoAcids: L/I
      codons: Ctt/Att
      dbsnpId: "1"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: HGNC
      hgncId: "11733"
      ccds: CCDS43968.1
      ensp: ENSP00000363453
      swissprot: Q8IYF3
      uniparc: UPI00002122F2
      genePheno: "1"
      sift:
        prediction: tolerated
        score: 0.18
      polyphen:
        prediction: benign
        score: 0.416
      domains:
        - id: seg
          source: Low_complexity_(Seg)
        - id: PTHR22904
          source: hmmpanther
        - id: PTHR22904
          source: hmmpanther
        - id: PF08631
          source: Pfam_domain
    - allele: T
      consequence: missense_variant
      impact: MODERATE
      symbol: TEX11
      gene: ENSG00000120498
      featureType: Transcript
      feature: ENST00000395889
      featureBiotype: protein_coding
      exon: 15/31
      hgvsc: "ENST00000395889.2:c.1168C>A"
      hgvsp: "ENSP00000379226.2:p.Leu390Ile"
      cdnaPosition: "1324"
      cdsPosition: "1168"
      proteinPosition: "390"
      aminoAcids: L/I
      codons: Ctt/Att
      dbsnpId: "1"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: HGNC
      hgncId: "11733"
      canonical: true
      ccds: CCDS35323.1
      ensp: ENSP00000379226
      swissprot: Q8IYF3
      uniparc: UPI000013CA89
      genePheno: "1"
      sift:
        prediction: tolerated
        score: 0.17
      polyphen:
        prediction: benign
        score: 0.105
      domains:
        - id: seg
          source: Low_complexity_(Seg)
        - id: PTHR22904
          source: hmmpanther
        - id: PTHR22904
          source: hmmpanther
        - id: PF08631
          source: Pfam_domain
  alleleCounts:
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          counts:
            overall:
              an: 12985
            xx:
              an: 10040
            xy:
              an: 2945
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 26680
            xx:
              an: 20200
            xy:
              an: 6480
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 7378
            xx:
              an: 4894
            xy:
              an: 2484
        - population: eas
          counts:
            overall:
              an: 13726
            xx:
              an: 9328
            xy:
              an: 4398
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 122
        - population: eas_oea
          counts:
            overall:
              an: 10719
        - population: eas_kor
          counts:
            overall:
              an: 2885
        - population: fin
          counts:
            overall:
              an: 15957
            xx:
              an: 10372
            xy:
              an: 5585
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 80706
              af: 0.0000123907
            xx:
              ac: 1
              an: 50044
              af: 0.0000199824
            xy:
              an: 30662
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 1979
        - population: nfe_est
          counts:
            overall:
              an: 194
        - population: nfe_nwe
          counts:
            overall:
              an: 30434
        - population: nfe_onf
          counts:
            overall:
              ac: 1
              an: 22340
              af: 0.0000447628
        - population: nfe_seu
          counts:
            overall:
              an: 6874
        - population: nfe_swe
          counts:
            overall:
              an: 18885
        - population: oth
          counts:
            overall:
              an: 4453
            xx:
              an: 2916
            xy:
              an: 1537
        - population: sas
          counts:
            overall:
              an: 17436
            xx:
              an: 7500
            xy:
              an: 9936
          faf95: 0
          faf99: 0
      bySex:
        overall:
          ac: 1
          an: 179321
          af: 0.00000557659
        xx:
          ac: 1
          an: 115294
          af: 0.00000867348
        xy:
          an: 64027
      raw:
        ac: 1
        an: 183512
        af: 0.00000544923
      popmax: nfe
      afPopmax: 0.0000123907
      acPopmax: 1
      anPopmax: 80706
      nhomaltPopmax: 0
    - cohort: controls
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 5598
            xx:
              an: 4228
            xy:
              an: 1370
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 13284
            xx:
              an: 10180
            xy:
              an: 3104
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 1727
            xx:
              an: 1212
            xy:
              an: 515
        - population: eas
          counts:
            overall:
              an: 6882
            xx:
              an: 4788
            xy:
              an: 2094
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 91
        - population: eas_oea
          counts:
            overall:
              an: 5329
        - population: eas_kor
          counts:
            overall:
              an: 1462
        - population: fin
          counts:
            overall:
              an: 9919
            xx:
              an: 6474
            xy:
              an: 3445
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 30573
              af: 0.0000327086
            xx:
              ac: 1
              an: 19134
              af: 0.000052263
            xy:
              an: 11439
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 507
        - population: nfe_est
          counts:
            overall:
              an: 51
        - population: nfe_nwe
          counts:
            overall:
              an: 10445
        - population: nfe_onf
          counts:
            overall:
              ac: 1
              an: 7420
              af: 0.000134771
        - population: nfe_seu
          counts:
            overall:
              an: 2751
        - population: nfe_swe
          counts:
            overall:
              an: 9399
        - population: oth
          counts:
            overall:
              an: 1425
            xx:
              an: 986
            xy:
              an: 439
        - population: sas
          counts:
            overall:
              an: 9216
            xx:
              an: 4190
            xy:
              an: 5026
          faf95: 0
          faf99: 0
      bySex:
        overall:
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          af: 0.0000127188
        xx:
          ac: 1
          an: 51192
          af: 0.0000195343
        xy:
          an: 27432
      raw:
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        an: 80343
        af: 0.0000124466
      popmax: nfe
      afPopmax: 0.0000327086
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      nhomaltPopmax: 0
    - cohort: non_cancer
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 11895
            xx:
              an: 9202
            xy:
              an: 2693
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 26428
            xx:
              an: 20016
            xy:
              an: 6412
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 6978
            xx:
              an: 4592
            xy:
              an: 2386
        - population: eas
          counts:
            overall:
              an: 13196
            xx:
              an: 8948
            xy:
              an: 4248
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 99
        - population: eas_oea
          counts:
            overall:
              an: 10242
        - population: eas_kor
          counts:
            overall:
              an: 2855
        - population: fin
          counts:
            overall:
              an: 15943
            xx:
              an: 10360
            xy:
              an: 5583
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 72394
              af: 0.0000138133
            xx:
              ac: 1
              an: 44222
              af: 0.0000226132
            xy:
              an: 28172
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 1876
        - population: nfe_est
          counts:
            overall:
              an: 119
        - population: nfe_nwe
          counts:
            overall:
              an: 28299
        - population: nfe_onf
          counts:
            overall:
              ac: 1
              an: 17626
              af: 0.0000567344
        - population: nfe_seu
          counts:
            overall:
              an: 6218
        - population: nfe_swe
          counts:
            overall:
              an: 18256
        - population: oth
          counts:
            overall:
              an: 4076
            xx:
              an: 2674
            xy:
              an: 1402
        - population: sas
          counts:
            overall:
              an: 17367
            xx:
              an: 7450
            xy:
              an: 9917
          faf95: 0
          faf99: 0
      bySex:
        overall:
          ac: 1
          an: 168277
          af: 0.00000594258
        xx:
          ac: 1
          an: 107464
          af: 0.00000930544
        xy:
          an: 60813
      raw:
        ac: 1
        an: 172308
        af: 0.00000580356
      popmax: nfe
      afPopmax: 0.0000138133
      acPopmax: 1
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      nhomaltPopmax: 0
    - cohort: non_neuro
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 12958
            xx:
              an: 10024
            xy:
              an: 2934
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 23674
            xx:
              an: 18198
            xy:
              an: 5476
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 4590
            xx:
              an: 3082
            xy:
              an: 1508
        - population: eas
          counts:
            overall:
              an: 10075
            xx:
              an: 6842
            xy:
              an: 3233
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 121
        - population: eas_oea
          counts:
            overall:
              an: 7071
        - population: eas_kor
          counts:
            overall:
              an: 2883
        - population: fin
          counts:
            overall:
              an: 12165
            xx:
              an: 7650
            xy:
              an: 4515
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 63622
              af: 0.0000157178
            xx:
              ac: 1
              an: 39734
              af: 0.0000251674
            xy:
              an: 23888
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 322
        - population: nfe_est
          counts:
            overall:
              an: 174
        - population: nfe_nwe
          counts:
            overall:
              an: 25729
        - population: nfe_onf
          counts:
            overall:
              ac: 1
              an: 20151
              af: 0.0000496253
        - population: nfe_seu
          counts:
            overall:
              an: 6486
        - population: nfe_swe
          counts:
            overall:
              an: 10760
        - population: oth
          counts:
            overall:
              an: 3561
            xx:
              an: 2380
            xy:
              an: 1181
        - population: sas
          counts:
            overall:
              an: 17431
            xx:
              an: 7498
            xy:
              an: 9933
          faf95: 0
          faf99: 0
      bySex:
        overall:
          ac: 1
          an: 148076
          af: 0.00000675329
        xx:
          ac: 1
          an: 95408
          af: 0.0000104813
        xy:
          an: 52668
      raw:
        ac: 1
        an: 151877
        af: 0.00000658428
      popmax: nfe
      afPopmax: 0.0000157178
      acPopmax: 1
      anPopmax: 63622
      nhomaltPopmax: 0
    - cohort: non_topmed
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 9592
            xx:
              an: 7318
            xy:
              an: 2274
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 26580
            xx:
              an: 20124
            xy:
              an: 6456
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 7314
            xx:
              an: 4848
            xy:
              an: 2466
        - population: eas
          counts:
            overall:
              an: 13724
            xx:
              an: 9328
            xy:
              an: 4396
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 122
        - population: eas_oea
          counts:
            overall:
              an: 10717
        - population: eas_kor
          counts:
            overall:
              an: 2885
        - population: fin
          counts:
            overall:
              an: 15955
            xx:
              an: 10370
            xy:
              an: 5585
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 79001
              af: 0.0000126581
            xx:
              ac: 1
              an: 48698
              af: 0.0000205347
            xy:
              an: 30303
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 1973
        - population: nfe_est
          counts:
            overall:
              an: 191
        - population: nfe_nwe
          counts:
            overall:
              an: 29529
        - population: nfe_onf
          counts:
            overall:
              ac: 1
              an: 21672
              af: 0.0000461425
        - population: nfe_seu
          counts:
            overall:
              an: 6807
        - population: nfe_swe
          counts:
            overall:
              an: 18829
        - population: oth
          counts:
            overall:
              an: 4390
            xx:
              an: 2866
            xy:
              an: 1524
        - population: sas
          counts:
            overall:
              an: 17436
            xx:
              an: 7500
            xy:
              an: 9936
          faf95: 0
          faf99: 0
      bySex:
        overall:
          ac: 1
          an: 173992
          af: 0.00000574739
        xx:
          ac: 1
          an: 111052
          af: 0.00000900479
        xy:
          an: 62940
      raw:
        ac: 1
        an: 178078
        af: 0.00000561552
      popmax: nfe
      afPopmax: 0.0000126581
      acPopmax: 1
      anPopmax: 79001
      nhomaltPopmax: 0
  nonpar: true
  rfInfo:
    rfTpProbability: 0.706202
  variantInfo:
    variantType: snv
    alleleType: snv
    nAltAlleles: 1
  qualityInfo:
    fs: 0
    inbreedingCoeff: -0.0005
    mq: 59.25
    mqRankSum: 0.735
    qd: 10.72
    readPosRankSum: 0.074
    baseQRankSum: -4.839
    clippingRankSum: 0.149
    sor: 0.652
    dp: 5945336
    vqslod: 1.16
    vqsrCulprit: MQ
    pabMax: 0.264893
  ageInfo:
    ageHistHomNSmaller: 0
    ageHistHomNLarger: 0
    ageHistHetNSmaller: 0
    ageHistHetNLarger: 1
  depthInfo:
    dpHistAllNLarger: 509
    dpHistAltNLarger: 1
- chrom: Y
  pos: 4967199
  refAllele: G
  altAllele: T
  vep:
    - allele: T
      consequence: missense_variant
      impact: MODERATE
      symbol: PCDH11Y
      gene: ENSG00000099715
      featureType: Transcript
      feature: ENST00000215473
      featureBiotype: protein_coding
      exon: 2/6
      hgvsc: "ENST00000215473.6:c.1580G>T"
      hgvsp: "ENSP00000215473.6:p.Ser527Ile"
      cdnaPosition: "1580"
      cdsPosition: "1580"
      proteinPosition: "527"
      aminoAcids: S/I
      codons: aGt/aTt
      dbsnpId: "1"
      strand: "1"
      variantClass: SNV
      minimised: "1"
      symbolSource: HGNC
      hgncId: "15813"
      ensp: ENSP00000215473
      trembl: Q70LR5&Q70LR4&J3QSR5
      uniparc: UPI0000D613B5
      sift:
        prediction: deleterious
      polyphen:
        prediction: possibly_damaging
        score: 0.462
      domains:
        - id: PS50268
          source: PROSITE_profiles
        - id: PTHR24027
          source: hmmpanther
        - id: PTHR24027
          source: hmmpanther
        - id: 2.60.40.60
          source: Gene3D
        - id: PF00028
          source: Pfam_domain
        - id: SM00112
          source: SMART_domains
        - id: SSF49313
          source: Superfamily_domains
        - id: PR00205
          source: Prints_domain
    - allele: T
      consequence: missense_variant
      impact: MODERATE
      symbol: PCDH11Y
      gene: ENSG00000099715
      featureType: Transcript
      feature: ENST00000333703
      featureBiotype: protein_coding
      exon: 5/6
      hgvsc: "ENST00000333703.4:c.1547G>T"
      hgvsp: "ENSP00000330552.4:p.Ser516Ile"
      cdnaPosition: "2060"
      cdsPosition: "1547"
      proteinPosition: "516"
      aminoAcids: S/I
      codons: aGt/aTt
      dbsnpId: "1"
      strand: "1"
      variantClass: SNV
      minimised: "1"
      symbolSource: HGNC
      hgncId: "15813"
      ccds: CCDS14776.1
      ensp: ENSP00000330552
      swissprot: Q9BZA8
      uniparc: UPI000006E1F2
      sift:
        prediction: deleterious
      polyphen:
        prediction: possibly_damaging
        score: 0.517
      domains:
        - id: PS50268
          source: PROSITE_profiles
        - id: PTHR24027
          source: hmmpanther
        - id: PTHR24027
          source: hmmpanther
        - id: 2.60.40.60
          source: Gene3D
        - id: PF00028
          source: Pfam_domain
        - id: SM00112
          source: SMART_domains
        - id: SSF49313
          source: Superfamily_domains
        - id: PR00205
          source: Prints_domain
    - allele: T
      consequence: missense_variant
      impact: MODERATE
      symbol: PCDH11Y
      gene: ENSG00000099715
      featureType: Transcript
      feature: ENST00000362095
      featureBiotype: protein_coding
      exon: 2/3
      hgvsc: "ENST00000362095.5:c.1580G>T"
      hgvsp: "ENSP00000355419.5:p.Ser527Ile"
      cdnaPosition: "2314"
      cdsPosition: "1580"
      proteinPosition: "527"
      aminoAcids: S/I
      codons: aGt/aTt
      dbsnpId: "1"
      strand: "1"
      variantClass: SNV
      minimised: "1"
      symbolSource: HGNC
      hgncId: "15813"
      canonical: true
      ccds: CCDS14777.1
      ensp: ENSP00000355419
      swissprot: Q9BZA8
      uniparc: UPI000006EF4D
      sift:
        prediction: deleterious
      polyphen:
        prediction: possibly_damaging
        score: 0.517
      domains:
        - id: PS50268
          source: PROSITE_profiles
        - id: PTHR24027
          source: hmmpanther
        - id: PTHR24027
          source: hmmpanther
        - id: PF00028
          source: Pfam_domain
        - id: 2.60.40.60
          source: Gene3D
        - id: SM00112
          source: SMART_domains
        - id: SSF49313
          source: Superfamily_domains
        - id: PR00205
          source: Prints_domain
    - allele: T
      consequence: missense_variant
      impact: MODERATE
      symbol: PCDH11Y
      gene: ENSG00000099715
      featureType: Transcript
      feature: ENST00000400457
      featureBiotype: protein_coding
      exon: 2/5
      hgvsc: "ENST00000400457.2:c.1515G>T"
      hgvsp: "ENSP00000383306.2:p.Ser506Ile"
      cdnaPosition: "1515"
      cdsPosition: "1517"
      proteinPosition: "506"
      aminoAcids: S/I
      codons: aGt/aTt
      dbsnpId: "1"
      strand: "1"
      flags: cds_start_NF
      variantClass: SNV
      minimised: "1"
      symbolSource: HGNC
      hgncId: "15813"
      ensp: ENSP00000383306
      trembl: Q70LR5&Q70LR4
      uniparc: UPI000059DC01
      sift:
        prediction: deleterious
      polyphen:
        prediction: possibly_damaging
        score: 0.517
      domains:
        - id: PS50268
          source: PROSITE_profiles
        - id: PTHR24027
          source: hmmpanther
        - id: PTHR24027
          source: hmmpanther
        - id: 2.60.40.60
          source: Gene3D
        - id: PF00028
          source: Pfam_domain
        - id: SM00112
          source: SMART_domains
        - id: SSF49313
          source: Superfamily_domains
        - id: PR00205
          source: Prints_domain
  alleleCounts:
    - byPopulation:
        - population: afr
          counts:
            overall:
              an: 3092
            xy:
              an: 3092
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 7157
            xy:
              an: 7157
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 2587
            xy:
              an: 2587
        - population: eas
          counts:
            overall:
              an: 4528
            xy:
              an: 4528
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 30
        - population: eas_oea
          counts:
            overall:
              an: 3567
        - population: eas_kor
          counts:
            overall:
              an: 931
        - population: fin
          counts:
            overall:
              an: 5636
            xy:
              an: 5636
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 31633
              af: 0.0000316126
            xy:
              ac: 1
              an: 31633
              af: 0.0000316126
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 683
        - population: nfe_est
          counts:
            overall:
              an: 45
        - population: nfe_nwe
          counts:
            overall:
              ac: 1
              an: 11269
              af: 0.000088739
        - population: nfe_onf
          counts:
            overall:
              an: 8237
        - population: nfe_seu
          counts:
            overall:
              an: 4442
        - population: nfe_swe
          counts:
            overall:
              an: 6957
        - population: oth
          counts:
            overall:
              an: 1603
            xy:
              an: 1603
        - population: sas
          counts:
            overall:
              an: 11530
            xy:
              an: 11530
          faf95: 0
          faf99: 0
      bySex:
        overall:
          ac: 1
          an: 67766
          af: 0.0000147567
        xy:
          ac: 1
          an: 67766
          af: 0.0000147567
      raw:
        ac: 1
        an: 67873
        af: 0.0000147334
      popmax: nfe
      afPopmax: 0.0000316126
      acPopmax: 1
      anPopmax: 31633
      nhomaltPopmax: 0
    - cohort: controls
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 1461
            xy:
              an: 1461
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 3441
            xy:
              an: 3441
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 552
            xy:
              an: 552
        - population: eas
          counts:
            overall:
              an: 2128
            xy:
              an: 2128
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 23
        - population: eas_oea
          counts:
            overall:
              an: 1680
        - population: eas_kor
          counts:
            overall:
              an: 425
        - population: fin
          counts:
            overall:
              an: 3459
            xy:
              an: 3459
        - population: nfe
          counts:
            overall:
              an: 11784
            xy:
              an: 11784
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 170
        - population: nfe_est
          counts:
            overall:
              an: 19
        - population: nfe_nwe
          counts:
            overall:
              an: 3904
        - population: nfe_onf
          counts:
            overall:
              an: 2485
        - population: nfe_seu
          counts:
            overall:
              an: 1914
        - population: nfe_swe
          counts:
            overall:
              an: 3292
        - population: oth
          counts:
            overall:
              an: 463
            xy:
              an: 463
        - population: sas
          counts:
            overall:
              an: 5736
            xy:
              an: 5736
          faf95: 0
          faf99: 0
      bySex:
        overall:
          an: 29024
        xy:
          an: 29024
      raw:
        an: 29057
    - cohort: non_cancer
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 2835
            xy:
              an: 2835
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 7083
            xy:
              an: 7083
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 2485
            xy:
              an: 2485
        - population: eas
          counts:
            overall:
              an: 4367
            xy:
              an: 4367
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 25
        - population: eas_oea
          counts:
            overall:
              an: 3425
        - population: eas_kor
          counts:
            overall:
              an: 917
        - population: fin
          counts:
            overall:
              an: 5634
            xy:
              an: 5634
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 29070
              af: 0.0000343997
            xy:
              ac: 1
              an: 29070
              af: 0.0000343997
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 644
        - population: nfe_est
          counts:
            overall:
              an: 38
        - population: nfe_nwe
          counts:
            overall:
              ac: 1
              an: 10713
              af: 0.0000933445
        - population: nfe_onf
          counts:
            overall:
              an: 6703
        - population: nfe_seu
          counts:
            overall:
              an: 4222
        - population: nfe_swe
          counts:
            overall:
              an: 6750
        - population: oth
          counts:
            overall:
              an: 1467
            xy:
              an: 1467
        - population: sas
          counts:
            overall:
              an: 11510
            xy:
              an: 11510
          faf95: 0
          faf99: 0
      bySex:
        overall:
          ac: 1
          an: 64451
          af: 0.0000155157
        xy:
          ac: 1
          an: 64451
          af: 0.0000155157
      raw:
        ac: 1
        an: 64542
        af: 0.0000154938
      popmax: nfe
      afPopmax: 0.0000343997
      acPopmax: 1
      anPopmax: 29070
      nhomaltPopmax: 0
    - cohort: non_neuro
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 3081
            xy:
              an: 3081
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 6125
            xy:
              an: 6125
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 1561
            xy:
              an: 1561
        - population: eas
          counts:
            overall:
              an: 3286
            xy:
              an: 3286
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 29
        - population: eas_oea
          counts:
            overall:
              an: 2326
        - population: eas_kor
          counts:
            overall:
              an: 931
        - population: fin
          counts:
            overall:
              an: 4541
            xy:
              an: 4541
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 24813
              af: 0.0000403015
            xy:
              ac: 1
              an: 24813
              af: 0.0000403015
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 127
        - population: nfe_est
          counts:
            overall:
              an: 39
        - population: nfe_nwe
          counts:
            overall:
              ac: 1
              an: 9238
              af: 0.000108249
        - population: nfe_onf
          counts:
            overall:
              an: 7306
        - population: nfe_seu
          counts:
            overall:
              an: 4272
        - population: nfe_swe
          counts:
            overall:
              an: 3831
        - population: oth
          counts:
            overall:
              an: 1235
            xy:
              an: 1235
        - population: sas
          counts:
            overall:
              an: 11527
            xy:
              an: 11527
          faf95: 0
          faf99: 0
      bySex:
        overall:
          ac: 1
          an: 56169
          af: 0.0000178034
        xy:
          ac: 1
          an: 56169
          af: 0.0000178034
      raw:
        ac: 1
        an: 56230
        af: 0.0000177841
      popmax: nfe
      afPopmax: 0.0000403015
      acPopmax: 1
      anPopmax: 24813
      nhomaltPopmax: 0
    - cohort: non_topmed
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 2342
            xy:
              an: 2342
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 7128
            xy:
              an: 7128
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 2569
            xy:
              an: 2569
        - population: eas
          counts:
            overall:
              an: 4526
            xy:
              an: 4526
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts:
            overall:
              an: 30
        - population: eas_oea
          counts:
            overall:
              an: 3565
        - population: eas_kor
          counts:
            overall:
              an: 931
        - population: fin
          counts:
            overall:
              an: 5636
            xy:
              an: 5636
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 31262
              af: 0.0000319877
            xy:
              ac: 1
              an: 31262
              af: 0.0000319877
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 681
        - population: nfe_est
          counts:
            overall:
              an: 44
        - population: nfe_nwe
          counts:
            overall:
              ac: 1
              an: 11063
              af: 0.0000903914
        - population: nfe_onf
          counts:
            overall:
              an: 8109
        - population: nfe_seu
          counts:
            overall:
              an: 4414
        - population: nfe_swe
          counts:
            overall:
              an: 6951
        - population: oth
          counts:
            overall:
              an: 1590
            xy:
              an: 1590
        - population: sas
          counts:
            overall:
              an: 11530
            xy:
              an: 11530
          faf95: 0
          faf99: 0
      bySex:
        overall:
          ac: 1
          an: 66583
          af: 0.0000150188
        xy:
          ac: 1
          an: 66583
          af: 0.0000150188
      raw:
        ac: 1
        an: 66690
        af: 0.0000149948
      popmax: nfe
      afPopmax: 0.0000319877
      acPopmax: 1
      anPopmax: 31262
      nhomaltPopmax: 0
  nonpar: true
  rfInfo:
    rfTpProbability: 0.779496
  variantInfo:
    variantType: snv
    alleleType: snv
    nAltAlleles: 1
  qualityInfo:
    fs: 0
    inbreedingCoeff: -0.0015
    mq: 54.15
    qd: 32.98
    vqsrNegativeTrainSite: true
    sor: 1.091
    dp: 3965717
    vqslod: 3.32
    vqsrCulprit: MQ
    segdup: true
  ageInfo:
    ageHistHomNSmaller: 0
    ageHistHomNLarger: 0
    ageHistHetNSmaller: 0
    ageHistHetNLarger: 0
  depthInfo:
    dpHistAllNLarger: 3
    dpHistAltNLarger: 1

