---
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: "MUTANT_DONOR_MES:8.16693067332728&DE_NOVO_DONOR_MES:-1.61109392005567&DE_NOVO_DONOR_MES_POS:-122&EXON_END:55505717&INTRON_START:55505718&DE_NOVO_DONOR_PROB:0.146539915246404&INTRON_END:55509515&DE_NOVO_DONOR_POS:-119&EXON_START:55505221"
    - allele: G
      consequence: missense_variant
      impact: MODERATE
      symbol: PCSK9
      gene: ENSG00000169174
      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&DE_NOVO_DONOR_MES:-1.61109392005567&MUTANT_DONOR_MES:8.16693067332728&INTRON_END:55509515&DE_NOVO_DONOR_POS:-119&EXON_END:55505717&DE_NOVO_DONOR_PROB:0.146539915246404&INTRON_START:55505718&EXON_START:55505431"
    - allele: G
      consequence: upstream_gene_variant
      impact: MODIFIER
      symbol: PCSK9
      gene: ENSG00000169174
      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: 8706
            xx:
              an: 3678
            xy:
              an: 5028
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 848
            xx:
              an: 414
            xy:
              an: 434
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 290
            xx:
              an: 80
            xy:
              an: 210
        - population: eas
          counts:
            overall:
              an: 1558
            xx:
              an: 538
            xy:
              an: 1020
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts: {}
        - population: eas_kor
          counts: {}
        - population: fin
          counts:
            overall:
              an: 3476
            xx:
              an: 1846
            xy:
              an: 1630
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 15428
              af: 0.0000648172
            xx:
              ac: 1
              an: 6806
              af: 0.000146929
            xy:
              an: 8622
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts: {}
        - population: nfe_est
          counts:
            overall:
              an: 4592
        - population: nfe_nwe
          counts:
            overall:
              an: 8594
        - population: nfe_onf
          counts:
            overall:
              an: 2136
        - population: nfe_seu
          counts:
            overall:
              ac: 1
              an: 106
              af: 0.00943396
        - population: nfe_swe
          counts: {}
        - population: oth
          counts:
            overall:
              an: 1086
            xx:
              an: 560
            xy:
              an: 526
        - population: sas
          counts: {}
      bySex:
        overall:
          ac: 1
          an: 31392
          af: 0.0000318552
        xx:
          ac: 1
          an: 13922
          af: 0.0000718288
        xy:
          an: 17470
      raw:
        ac: 1
        an: 31416
        af: 0.0000318309
      popmax: nfe
      afPopmax: 0.0000648172
      acPopmax: 1
      anPopmax: 15428
      nhomaltPopmax: 0
    - cohort: controls
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 2570
            xx:
              an: 1164
            xy:
              an: 1406
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 246
            xx:
              an: 120
            xy:
              an: 126
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 38
            xx:
              an: 24
            xy:
              an: 14
        - population: eas
          counts:
            overall:
              an: 914
            xx:
              an: 342
            xy:
              an: 572
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts: {}
        - population: eas_kor
          counts: {}
        - population: fin
          counts:
            overall:
              an: 1162
            xx:
              an: 556
            xy:
              an: 606
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 5518
              af: 0.000181225
            xx:
              ac: 1
              an: 2576
              af: 0.000388199
            xy:
              an: 2942
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts: {}
        - population: nfe_est
          counts:
            overall:
              an: 4104
        - population: nfe_nwe
          counts:
            overall:
              an: 920
        - population: nfe_onf
          counts:
            overall:
              an: 438
        - population: nfe_seu
          counts:
            overall:
              ac: 1
              an: 56
              af: 0.0178571
        - population: nfe_swe
          counts: {}
        - population: oth
          counts:
            overall:
              an: 424
            xx:
              an: 226
            xy:
              an: 198
        - population: sas
          counts: {}
      bySex:
        overall:
          ac: 1
          an: 10872
          af: 0.0000919794
        xx:
          ac: 1
          an: 5008
          af: 0.000199681
        xy:
          an: 5864
      raw:
        ac: 1
        an: 10884
        af: 0.000091878
      popmax: nfe
      afPopmax: 0.000181225
      acPopmax: 1
      anPopmax: 5518
      nhomaltPopmax: 0
    - cohort: non_cancer
      byPopulation:
        - population: afr
          counts: {}
          faf95: 0
          faf99: 0
        - population: amr
          counts: {}
          faf95: 0
          faf99: 0
        - population: asj
          counts: {}
        - population: eas
          counts: {}
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts: {}
        - population: eas_kor
          counts: {}
        - population: fin
          counts: {}
        - population: nfe
          counts: {}
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts: {}
        - population: nfe_est
          counts: {}
        - population: nfe_nwe
          counts: {}
        - population: nfe_onf
          counts: {}
        - population: nfe_seu
          counts: {}
        - population: nfe_swe
          counts: {}
        - population: oth
          counts: {}
        - population: sas
          counts: {}
      bySex: {}
    - cohort: non_neuro
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 3384
            xx:
              an: 1778
            xy:
              an: 1606
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 554
            xx:
              an: 310
            xy:
              an: 244
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 246
            xx:
              an: 60
            xy:
              an: 186
        - population: eas
          counts:
            overall:
              an: 1558
            xx:
              an: 538
            xy:
              an: 1020
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts: {}
        - population: eas_kor
          counts: {}
        - population: fin
          counts:
            overall:
              an: 1164
            xx:
              an: 558
            xy:
              an: 606
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 13618
              af: 0.0000734322
            xx:
              ac: 1
              an: 5982
              af: 0.000167168
            xy:
              an: 7636
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts: {}
        - population: nfe_est
          counts:
            overall:
              an: 4146
        - population: nfe_nwe
          counts:
            overall:
              an: 7698
        - population: nfe_onf
          counts:
            overall:
              an: 1720
        - population: nfe_seu
          counts:
            overall:
              ac: 1
              an: 54
              af: 0.0185185
        - population: nfe_swe
          counts: {}
        - population: oth
          counts:
            overall:
              an: 734
            xx:
              an: 364
            xy:
              an: 370
        - population: sas
          counts: {}
      bySex:
        overall:
          ac: 1
          an: 21258
          af: 0.0000470411
        xx:
          ac: 1
          an: 9590
          af: 0.000104275
        xy:
          an: 11668
      raw:
        ac: 1
        an: 21272
        af: 0.0000470102
      popmax: nfe
      afPopmax: 0.0000734322
      acPopmax: 1
      anPopmax: 13618
      nhomaltPopmax: 0
    - cohort: non_topmed
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 8544
            xx:
              an: 3610
            xy:
              an: 4934
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 810
            xx:
              an: 394
            xy:
              an: 416
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 138
            xx:
              an: 62
            xy:
              an: 76
        - population: eas
          counts:
            overall:
              an: 1520
            xx:
              an: 520
            xy:
              an: 1000
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts: {}
        - population: eas_kor
          counts: {}
        - population: fin
          counts:
            overall:
              an: 3476
            xx:
              an: 1846
            xy:
              an: 1630
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 11088
              af: 0.0000901876
            xx:
              ac: 1
              an: 5610
              af: 0.000178253
            xy:
              an: 5478
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts: {}
        - population: nfe_est
          counts:
            overall:
              an: 4570
        - population: nfe_nwe
          counts:
            overall:
              an: 4898
        - population: nfe_onf
          counts:
            overall:
              an: 1514
        - population: nfe_seu
          counts:
            overall:
              ac: 1
              an: 106
              af: 0.00943396
        - population: nfe_swe
          counts: {}
        - population: oth
          counts:
            overall:
              an: 1010
            xx:
              an: 544
            xy:
              an: 466
        - population: sas
          counts: {}
      bySex:
        overall:
          ac: 1
          an: 26586
          af: 0.0000376138
        xx:
          ac: 1
          an: 12586
          af: 0.0000794534
        xy:
          an: 14000
      raw:
        ac: 1
        an: 26608
        af: 0.0000375827
      popmax: nfe
      afPopmax: 0.0000901876
      acPopmax: 1
      anPopmax: 11088
      nhomaltPopmax: 0
  rfInfo:
    rfTpProbability: 0.77474
  variantInfo:
    variantType: snv
    alleleType: snv
    nAltAlleles: 1
  qualityInfo:
    fs: 1.515
    inbreedingCoeff: 0.0198
    mq: 59.95
    mqRankSum: -1.385
    qd: 12.71
    readPosRankSum: 0.308
    vqsrNegativeTrainSite: true
    baseQRankSum: 2.21
    clippingRankSum: 1.33
    sor: 1.022
    dp: 696568
    vqslod: -2.305
    vqsrCulprit: MQ
    pabMax: 1
  ageInfo:
    ageHistHomNSmaller: 0
    ageHistHomNLarger: 0
    ageHistHetNSmaller: 0
    ageHistHetNLarger: 0
  depthInfo:
    dpHistAllNLarger: 2
    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: 154
              an: 8702
              af: 0.0176971
            xx:
              ac: 67
              an: 3674
              af: 0.0182363
            xy:
              ac: 87
              an: 5028
              af: 0.0173031
          faf95: 0.0154185
          faf99: 0.0154183
        - population: amr
          counts:
            overall:
              an: 848
            xx:
              an: 414
            xy:
              an: 434
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 290
            xx:
              an: 80
            xy:
              an: 210
        - population: eas
          counts:
            overall:
              an: 1560
            xx:
              an: 538
            xy:
              an: 1022
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts: {}
        - population: eas_kor
          counts: {}
        - population: fin
          counts:
            overall:
              an: 3476
            xx:
              an: 1846
            xy:
              an: 1630
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 15420
              af: 0.0000648508
            xx:
              an: 6800
            xy:
              ac: 1
              an: 8620
              af: 0.000116009
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts: {}
        - population: nfe_est
          counts:
            overall:
              an: 4584
        - population: nfe_nwe
          counts:
            overall:
              ac: 1
              an: 8592
              af: 0.000116387
        - population: nfe_onf
          counts:
            overall:
              an: 2138
        - population: nfe_seu
          counts:
            overall:
              an: 106
        - population: nfe_swe
          counts: {}
        - population: oth
          counts:
            overall:
              ac: 1
              an: 1086
              af: 0.00092081
            xx:
              an: 560
            xy:
              ac: 1
              an: 526
              af: 0.00190114
        - population: sas
          counts: {}
      bySex:
        overall:
          ac: 156
          an: 31382
          af: 0.004971
        xx:
          ac: 67
          an: 13912
          af: 0.00481599
        xy:
          ac: 89
          an: 17470
          af: 0.00509445
      raw:
        ac: 156
        an: 31416
        af: 0.00496562
      popmax: afr
      afPopmax: 0.0176971
      acPopmax: 154
      anPopmax: 8702
      nhomaltPopmax: 0
    - cohort: controls
      byPopulation:
        - population: afr
          counts:
            overall:
              ac: 40
              an: 2572
              af: 0.0155521
            xx:
              ac: 25
              an: 1164
              af: 0.0214777
            xy:
              ac: 15
              an: 1408
              af: 0.0106534
          faf95: 0.0154185
          faf99: 0.0154183
        - population: amr
          counts:
            overall:
              an: 246
            xx:
              an: 120
            xy:
              an: 126
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 38
            xx:
              an: 24
            xy:
              an: 14
        - population: eas
          counts:
            overall:
              an: 916
            xx:
              an: 342
            xy:
              an: 574
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts: {}
        - population: eas_kor
          counts: {}
        - population: fin
          counts:
            overall:
              an: 1162
            xx:
              an: 556
            xy:
              an: 606
        - population: nfe
          counts:
            overall:
              an: 5514
            xx:
              an: 2576
            xy:
              an: 2938
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts: {}
        - population: nfe_est
          counts:
            overall:
              an: 4096
        - population: nfe_nwe
          counts:
            overall:
              an: 922
        - population: nfe_onf
          counts:
            overall:
              an: 440
        - population: nfe_seu
          counts:
            overall:
              an: 56
        - population: nfe_swe
          counts: {}
        - population: oth
          counts:
            overall:
              an: 422
            xx:
              an: 224
            xy:
              an: 198
        - population: sas
          counts: {}
      bySex:
        overall:
          ac: 40
          an: 10870
          af: 0.00367985
        xx:
          ac: 25
          an: 5006
          af: 0.00499401
        xy:
          ac: 15
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          af: 0.00255798
      raw:
        ac: 40
        an: 10884
        af: 0.00367512
      popmax: afr
      afPopmax: 0.0155521
      acPopmax: 40
      anPopmax: 2572
      nhomaltPopmax: 0
    - cohort: non_cancer
      byPopulation:
        - population: afr
          counts: {}
          faf95: 0.0154185
          faf99: 0.0154183
        - population: amr
          counts: {}
          faf95: 0
          faf99: 0
        - population: asj
          counts: {}
        - population: eas
          counts: {}
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts: {}
        - population: eas_kor
          counts: {}
        - population: fin
          counts: {}
        - population: nfe
          counts: {}
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts: {}
        - population: nfe_est
          counts: {}
        - population: nfe_nwe
          counts: {}
        - population: nfe_onf
          counts: {}
        - population: nfe_seu
          counts: {}
        - population: nfe_swe
          counts: {}
        - population: oth
          counts: {}
        - population: sas
          counts: {}
      bySex: {}
    - cohort: non_neuro
      byPopulation:
        - population: afr
          counts:
            overall:
              ac: 48
              an: 3386
              af: 0.014176
            xx:
              ac: 31
              an: 1778
              af: 0.0174353
            xy:
              ac: 17
              an: 1608
              af: 0.0105721
          faf95: 0.0154185
          faf99: 0.0154183
        - population: amr
          counts:
            overall:
              an: 554
            xx:
              an: 310
            xy:
              an: 244
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 246
            xx:
              an: 60
            xy:
              an: 186
        - population: eas
          counts:
            overall:
              an: 1560
            xx:
              an: 538
            xy:
              an: 1022
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts: {}
        - population: eas_kor
          counts: {}
        - population: fin
          counts:
            overall:
              an: 1164
            xx:
              an: 558
            xy:
              an: 606
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 13610
              af: 0.0000734754
            xx:
              an: 5976
            xy:
              ac: 1
              an: 7634
              af: 0.000130993
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts: {}
        - population: nfe_est
          counts:
            overall:
              an: 4138
        - population: nfe_nwe
          counts:
            overall:
              ac: 1
              an: 7696
              af: 0.000129938
        - population: nfe_onf
          counts:
            overall:
              an: 1722
        - population: nfe_seu
          counts:
            overall:
              an: 54
        - population: nfe_swe
          counts: {}
        - population: oth
          counts:
            overall:
              an: 732
            xx:
              an: 362
            xy:
              an: 370
        - population: sas
          counts: {}
      bySex:
        overall:
          ac: 49
          an: 21252
          af: 0.00230567
        xx:
          ac: 31
          an: 9582
          af: 0.00323523
        xy:
          ac: 18
          an: 11670
          af: 0.00154242
      raw:
        ac: 49
        an: 21272
        af: 0.0023035
      popmax: afr
      afPopmax: 0.014176
      acPopmax: 48
      anPopmax: 3386
      nhomaltPopmax: 0
    - cohort: non_topmed
      byPopulation:
        - population: afr
          counts:
            overall:
              ac: 152
              an: 8540
              af: 0.0177986
            xx:
              ac: 66
              an: 3606
              af: 0.0183028
            xy:
              ac: 86
              an: 4934
              af: 0.0174301
          faf95: 0.0154185
          faf99: 0.0154183
        - population: amr
          counts:
            overall:
              an: 810
            xx:
              an: 394
            xy:
              an: 416
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 138
            xx:
              an: 62
            xy:
              an: 76
        - population: eas
          counts:
            overall:
              an: 1522
            xx:
              an: 520
            xy:
              an: 1002
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts: {}
        - population: eas_kor
          counts: {}
        - population: fin
          counts:
            overall:
              an: 3476
            xx:
              an: 1846
            xy:
              an: 1630
        - population: nfe
          counts:
            overall:
              ac: 1
              an: 11080
              af: 0.0000902527
            xx:
              an: 5606
            xy:
              ac: 1
              an: 5474
              af: 0.000182682
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts: {}
        - population: nfe_est
          counts:
            overall:
              an: 4562
        - population: nfe_nwe
          counts:
            overall:
              ac: 1
              an: 4896
              af: 0.000204248
        - population: nfe_onf
          counts:
            overall:
              an: 1516
        - population: nfe_seu
          counts:
            overall:
              an: 106
        - population: nfe_swe
          counts: {}
        - population: oth
          counts:
            overall:
              ac: 1
              an: 1010
              af: 0.000990099
            xx:
              an: 544
            xy:
              ac: 1
              an: 466
              af: 0.00214592
        - population: sas
          counts: {}
      bySex:
        overall:
          ac: 154
          an: 26576
          af: 0.0057947
        xx:
          ac: 66
          an: 12578
          af: 0.00524726
        xy:
          ac: 88
          an: 13998
          af: 0.00628661
      raw:
        ac: 154
        an: 26608
        af: 0.00578773
      popmax: afr
      afPopmax: 0.0177986
      acPopmax: 152
      anPopmax: 8540
      nhomaltPopmax: 0
  rfInfo:
    rfTpProbability: 0.952127
    rfPositiveLabel: true
    rfLabel: TP
    rfTrain: true
  variantInfo:
    variantType: indel
    alleleType: ins
    nAltAlleles: 1
  qualityInfo:
    fs: 0.52
    inbreedingCoeff: -0.0043
    mq: 60
    mqRankSum: -0.017
    qd: 15.91
    readPosRankSum: 0.122
    vqsrPositiveTrainSite: true
    baseQRankSum: -0.161
    clippingRankSum: -0.129
    sor: 0.654
    dp: 660105
    vqslod: 4.41
    vqsrCulprit: FS
    pabMax: 1
  ageInfo:
    ageHistHomNSmaller: 0
    ageHistHomNLarger: 0
    ageHistHetNSmaller: 64
    ageHistHetNLarger: 2
  depthInfo:
    dpHistAllNLarger: 1
    dpHistAltNLarger: 0
- chrom: X
  pos: 69902634
  refAllele: C
  altAllele: T
  vep:
    - allele: T
      consequence: missense_variant
      impact: MODERATE
      symbol: TEX11
      gene: ENSG00000120498
      featureType: Transcript
      feature: ENST00000344304
      featureBiotype: protein_coding
      exon: 13/29
      hgvsc: "ENST00000344304.3:c.1091G>A"
      hgvsp: "ENSP00000340995.3:p.Arg364His"
      cdnaPosition: "1091"
      cdsPosition: "1091"
      proteinPosition: "364"
      aminoAcids: R/H
      codons: cGt/cAt
      existingVariation: rs201471690
      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: 1
      polyphen:
        prediction: benign
        score: 0.007
      domains:
        - id: PTHR22904
          source: hmmpanther
        - id: PTHR22904
          source: hmmpanther
        - id: PF08631
          source: Pfam_domain
      gmaf: 0.0005
      afrMaf: 0
      amrMaf: 0.0008
      easMaf: 0
      eurMaf: 0
      sasMaf: 0.001
      aaMaf: 0
      exacAdjMaf: 0
      exacAfrMaf: 0.00003295
      exacAmrMaf: 0.0001237
      exacEasMaf: 0.00002495
      exacFinMaf: 0
      exacNfeMaf: 0
      exacOthMaf: 0.00002306
      exacSasMaf: 0
      lofInfo: "EXON_START:69902524&EXON_END:69902675&DE_NOVO_DONOR_MES:0.0381663094165419&DE_NOVO_DONOR_POS:-108&DE_NOVO_DONOR_MES_POS:-108&MUTANT_DONOR_MES:6.38837132164763&DE_NOVO_DONOR_PROB:0.0218748740634797&INTRON_END:69902523&INTRON_START:69898740"
    - allele: T
      consequence: missense_variant
      impact: MODERATE
      symbol: TEX11
      gene: ENSG00000120498
      featureType: Transcript
      feature: ENST00000374320
      featureBiotype: protein_coding
      exon: 3/19
      hgvsc: "ENST00000374320.2:c.116G>A"
      hgvsp: "ENSP00000363440.2:p.Arg39His"
      cdnaPosition: "338"
      cdsPosition: "116"
      proteinPosition: "39"
      aminoAcids: R/H
      codons: cGt/cAt
      existingVariation: rs201471690
      dbsnpId: "1"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: HGNC
      hgncId: "11733"
      ensp: ENSP00000363440
      swissprot: Q8IYF3
      uniparc: UPI00004A2D6C
      genePheno: "1"
      sift:
        prediction: tolerated
        score: 1
      polyphen:
        prediction: benign
        score: 0.007
      domains:
        - id: PTHR22904
          source: hmmpanther
        - id: PTHR22904
          source: hmmpanther
        - id: PF08631
          source: Pfam_domain
      gmaf: 0.0005
      afrMaf: 0
      amrMaf: 0.0008
      easMaf: 0
      eurMaf: 0
      sasMaf: 0.001
      aaMaf: 0
      exacAdjMaf: 0
      exacAfrMaf: 0.00003295
      exacAmrMaf: 0.0001237
      exacEasMaf: 0.00002495
      exacFinMaf: 0
      exacNfeMaf: 0
      exacOthMaf: 0.00002306
      exacSasMaf: 0
      lofInfo: "INTRON_END:69902523&DE_NOVO_DONOR_PROB:0.0218748740634797&MUTANT_DONOR_MES:6.38837132164763&INTRON_START:69898740&EXON_START:69902524&EXON_END:69902675&DE_NOVO_DONOR_MES:0.0381663094165419&DE_NOVO_DONOR_POS:-108&DE_NOVO_DONOR_MES_POS:-108"
    - allele: T
      consequence: missense_variant
      impact: MODERATE
      symbol: TEX11
      gene: ENSG00000120498
      featureType: Transcript
      feature: ENST00000374333
      featureBiotype: protein_coding
      exon: 14/30
      hgvsc: "ENST00000374333.2:c.1046G>A"
      hgvsp: "ENSP00000363453.2:p.Arg349His"
      cdnaPosition: "1145"
      cdsPosition: "1046"
      proteinPosition: "349"
      aminoAcids: R/H
      codons: cGt/cAt
      existingVariation: rs201471690
      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: 1
      polyphen:
        prediction: benign
        score: 0.003
      domains:
        - id: PTHR22904
          source: hmmpanther
        - id: PTHR22904
          source: hmmpanther
        - id: PF08631
          source: Pfam_domain
      gmaf: 0.0005
      afrMaf: 0
      amrMaf: 0.0008
      easMaf: 0
      eurMaf: 0
      sasMaf: 0.001
      aaMaf: 0
      exacAdjMaf: 0
      exacAfrMaf: 0.00003295
      exacAmrMaf: 0.0001237
      exacEasMaf: 0.00002495
      exacFinMaf: 0
      exacNfeMaf: 0
      exacOthMaf: 0.00002306
      exacSasMaf: 0
      lofInfo: "DE_NOVO_DONOR_POS:-108&DE_NOVO_DONOR_MES_POS:-108&EXON_START:69902524&EXON_END:69902675&DE_NOVO_DONOR_MES:0.0381663094165419&INTRON_START:69898740&INTRON_END:69902523&DE_NOVO_DONOR_PROB:0.0218748740634797&MUTANT_DONOR_MES:6.38837132164763"
    - allele: T
      consequence: missense_variant
      impact: MODERATE
      symbol: TEX11
      gene: ENSG00000120498
      featureType: Transcript
      feature: ENST00000395889
      featureBiotype: protein_coding
      exon: 15/31
      hgvsc: "ENST00000395889.2:c.1091G>A"
      hgvsp: "ENSP00000379226.2:p.Arg364His"
      cdnaPosition: "1247"
      cdsPosition: "1091"
      proteinPosition: "364"
      aminoAcids: R/H
      codons: cGt/cAt
      existingVariation: rs201471690
      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: 1
      polyphen:
        prediction: benign
        score: 0.007
      domains:
        - id: PTHR22904
          source: hmmpanther
        - id: PTHR22904
          source: hmmpanther
        - id: PF08631
          source: Pfam_domain
      gmaf: 0.0005
      afrMaf: 0
      amrMaf: 0.0008
      easMaf: 0
      eurMaf: 0
      sasMaf: 0.001
      aaMaf: 0
      exacAdjMaf: 0
      exacAfrMaf: 0.00003295
      exacAmrMaf: 0.0001237
      exacEasMaf: 0.00002495
      exacFinMaf: 0
      exacNfeMaf: 0
      exacOthMaf: 0.00002306
      exacSasMaf: 0
      lofInfo: "INTRON_END:69902523&DE_NOVO_DONOR_PROB:0.0218748740634797&MUTANT_DONOR_MES:6.38837132164763&INTRON_START:69898740&EXON_END:69902675&EXON_START:69902524&DE_NOVO_DONOR_MES:0.0381663094165419&DE_NOVO_DONOR_POS:-108&DE_NOVO_DONOR_MES_POS:-108"
  alleleCounts:
    - byPopulation:
        - population: afr
          counts:
            overall:
              ac: 1
              an: 5881
              af: 0.000170039
            xx:
              ac: 1
              an: 3682
              af: 0.000271592
            xy:
              an: 2199
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 612
            xx:
              an: 414
            xy:
              an: 198
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 175
            xx:
              an: 80
            xy:
              an: 95
        - population: eas
          counts:
            overall:
              an: 1008
            xx:
              an: 538
            xy:
              an: 470
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts: {}
        - population: eas_kor
          counts: {}
        - population: fin
          counts:
            overall:
              an: 2574
            xx:
              an: 1844
            xy:
              an: 730
        - population: nfe
          counts:
            overall:
              an: 10810
            xx:
              an: 6806
            xy:
              an: 4004
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts: {}
        - population: nfe_est
          counts:
            overall:
              an: 3312
        - population: nfe_nwe
          counts:
            overall:
              an: 5938
        - population: nfe_onf
          counts:
            overall:
              an: 1486
        - population: nfe_seu
          counts:
            overall:
              an: 74
        - population: nfe_swe
          counts: {}
        - population: oth
          counts:
            overall:
              an: 797
            xx:
              an: 562
            xy:
              an: 235
        - population: sas
          counts: {}
      bySex:
        overall:
          ac: 1
          an: 21857
          af: 0.0000457519
        xx:
          ac: 1
          an: 13926
          af: 0.0000718081
        xy:
          an: 7931
      raw:
        ac: 1
        an: 22675
        af: 0.0000441014
      popmax: afr
      afPopmax: 0.000170039
      acPopmax: 1
      anPopmax: 5881
      nhomaltPopmax: 0
    - cohort: controls
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 1779
            xx:
              an: 1166
            xy:
              an: 613
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 177
            xx:
              an: 120
            xy:
              an: 57
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 31
            xx:
              an: 24
            xy:
              an: 7
        - population: eas
          counts:
            overall:
              an: 611
            xx:
              an: 342
            xy:
              an: 269
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts: {}
        - population: eas_kor
          counts: {}
        - population: fin
          counts:
            overall:
              an: 828
            xx:
              an: 554
            xy:
              an: 274
        - population: nfe
          counts:
            overall:
              an: 3888
            xx:
              an: 2578
            xy:
              an: 1310
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts: {}
        - population: nfe_est
          counts:
            overall:
              an: 2928
        - population: nfe_nwe
          counts:
            overall:
              an: 610
        - population: nfe_onf
          counts:
            overall:
              an: 310
        - population: nfe_seu
          counts:
            overall:
              an: 40
        - population: nfe_swe
          counts: {}
        - population: oth
          counts:
            overall:
              an: 313
            xx:
              an: 226
            xy:
              an: 87
        - population: sas
          counts: {}
      bySex:
        overall:
          an: 7627
        xx:
          an: 5010
        xy:
          an: 2617
      raw:
        an: 7950
    - cohort: non_cancer
      byPopulation:
        - population: afr
          counts: {}
          faf95: 0
          faf99: 0
        - population: amr
          counts: {}
          faf95: 0
          faf99: 0
        - population: asj
          counts: {}
        - population: eas
          counts: {}
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts: {}
        - population: eas_kor
          counts: {}
        - population: fin
          counts: {}
        - population: nfe
          counts: {}
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts: {}
        - population: nfe_est
          counts: {}
        - population: nfe_nwe
          counts: {}
        - population: nfe_onf
          counts: {}
        - population: nfe_seu
          counts: {}
        - population: nfe_swe
          counts: {}
        - population: oth
          counts: {}
        - population: sas
          counts: {}
      bySex: {}
    - cohort: non_neuro
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 2486
            xx:
              an: 1780
            xy:
              an: 706
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 420
            xx:
              an: 310
            xy:
              an: 110
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 148
            xx:
              an: 60
            xy:
              an: 88
        - population: eas
          counts:
            overall:
              an: 1008
            xx:
              an: 538
            xy:
              an: 470
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts: {}
        - population: eas_kor
          counts: {}
        - population: fin
          counts:
            overall:
              an: 830
            xx:
              an: 556
            xy:
              an: 274
        - population: nfe
          counts:
            overall:
              an: 9531
            xx:
              an: 5982
            xy:
              an: 3549
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts: {}
        - population: nfe_est
          counts:
            overall:
              an: 2957
        - population: nfe_nwe
          counts:
            overall:
              an: 5329
        - population: nfe_onf
          counts:
            overall:
              an: 1206
        - population: nfe_seu
          counts:
            overall:
              an: 39
        - population: nfe_swe
          counts: {}
        - population: oth
          counts:
            overall:
              an: 526
            xx:
              an: 364
            xy:
              an: 162
        - population: sas
          counts: {}
      bySex:
        overall:
          an: 14949
        xx:
          an: 9590
        xy:
          an: 5359
      raw:
        an: 15435
    - cohort: non_topmed
      byPopulation:
        - population: afr
          counts:
            overall:
              ac: 1
              an: 5767
              af: 0.0001734
            xx:
              ac: 1
              an: 3614
              af: 0.000276702
            xy:
              an: 2153
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 583
            xx:
              an: 394
            xy:
              an: 189
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 93
            xx:
              an: 62
            xy:
              an: 31
        - population: eas
          counts:
            overall:
              an: 981
            xx:
              an: 520
            xy:
              an: 461
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts: {}
        - population: eas_kor
          counts: {}
        - population: fin
          counts:
            overall:
              an: 2574
            xx:
              an: 1844
            xy:
              an: 730
        - population: nfe
          counts:
            overall:
              an: 8098
            xx:
              an: 5610
            xy:
              an: 2488
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts: {}
        - population: nfe_est
          counts:
            overall:
              an: 3297
        - population: nfe_nwe
          counts:
            overall:
              an: 3627
        - population: nfe_onf
          counts:
            overall:
              an: 1100
        - population: nfe_seu
          counts:
            overall:
              an: 74
        - population: nfe_swe
          counts: {}
        - population: oth
          counts:
            overall:
              an: 752
            xx:
              an: 546
            xy:
              an: 206
        - population: sas
          counts: {}
      bySex:
        overall:
          ac: 1
          an: 18848
          af: 0.000053056
        xx:
          ac: 1
          an: 12590
          af: 0.0000794281
        xy:
          an: 6258
      raw:
        ac: 1
        an: 19603
        af: 0.0000510126
      popmax: afr
      afPopmax: 0.0001734
      acPopmax: 1
      anPopmax: 5767
      nhomaltPopmax: 0
  nonpar: true
  rfInfo:
    rfTpProbability: 0.208912
  variantInfo:
    variantType: snv
    alleleType: snv
    nAltAlleles: 1
  qualityInfo:
    fs: 3.617
    inbreedingCoeff: -0.0007
    mq: 60
    mqRankSum: 0.344
    qd: 4.62
    readPosRankSum: 1.23
    baseQRankSum: 1.87
    clippingRankSum: 1.62
    sor: 1.358
    dp: 464079
    vqslod: 13.71
    vqsrCulprit: MQ
    pabMax: 0.0871586
  ageInfo:
    ageHistHomNSmaller: 0
    ageHistHomNLarger: 0
    ageHistHetNSmaller: 1
    ageHistHetNLarger: 0
  depthInfo:
    dpHistAllNLarger: 0
    dpHistAltNLarger: 0

