---
source: src/pbs/gnomad/gnomad2.rs
expression: records
---
- chrom: chr1
  pos: 138653
  refAllele: C
  altAllele: G
  vep:
    - allele: G
      consequence: synonymous_variant
      impact: LOW
      symbol: AL627309.1
      gene: ENSG00000237683
      featureType: Transcript
      feature: ENST00000423372
      featureBiotype: protein_coding
      exon: 1/2
      hgvsc: "ENST00000423372.3:c.657G>C"
      hgvsp: "ENST00000423372.3:c.657G>C(p.=)"
      cdnaPosition: "727"
      cdsPosition: "657"
      proteinPosition: "219"
      aminoAcids: G
      codons: ggG/ggC
      dbsnpId: "1"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: Clone_based_ensembl_gene
      canonical: true
      ensp: ENSP00000473460
      trembl: R4GN28&B7Z7W4
      uniparc: UPI0002C88512
    - allele: G
      consequence: downstream_gene_variant
      impact: MODIFIER
      symbol: CICP27
      gene: ENSG00000233750
      featureType: Transcript
      feature: ENST00000442987
      featureBiotype: processed_pseudogene
      dbsnpId: "1"
      distance: "3817"
      strand: "1"
      variantClass: SNV
      minimised: "1"
      symbolSource: HGNC
      hgncId: "48835"
      canonical: true
    - allele: G
      consequence: downstream_gene_variant
      impact: MODIFIER
      symbol: RP11-34P13.13
      gene: ENSG00000241860
      featureType: Transcript
      feature: ENST00000484859
      featureBiotype: antisense
      dbsnpId: "1"
      distance: "2821"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: Clone_based_vega_gene
      canonical: true
    - allele: G
      consequence: downstream_gene_variant
      impact: MODIFIER
      symbol: RP11-34P13.13
      gene: ENSG00000241860
      featureType: Transcript
      feature: ENST00000490997
      featureBiotype: antisense
      dbsnpId: "1"
      distance: "4155"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: Clone_based_vega_gene
    - allele: G
      consequence: downstream_gene_variant
      impact: MODIFIER
      symbol: RP11-34P13.14
      gene: ENSG00000239906
      featureType: Transcript
      feature: ENST00000493797
      featureBiotype: antisense
      dbsnpId: "1"
      distance: "1137"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: Clone_based_vega_gene
      canonical: true
    - allele: G
      consequence: upstream_gene_variant
      impact: MODIFIER
      symbol: RP11-34P13.15
      gene: ENSG00000268903
      featureType: Transcript
      feature: ENST00000494149
      featureBiotype: processed_pseudogene
      dbsnpId: "1"
      distance: "2758"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: Clone_based_vega_gene
      canonical: true
    - allele: G
      consequence: upstream_gene_variant
      impact: MODIFIER
      symbol: RP11-34P13.16
      gene: ENSG00000269981
      featureType: Transcript
      feature: ENST00000595919
      featureBiotype: processed_pseudogene
      dbsnpId: "1"
      distance: "688"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: Clone_based_vega_gene
      canonical: true
    - allele: G
      consequence: regulatory_region_variant
      impact: MODIFIER
      featureType: RegulatoryFeature
      feature: ENSR00000668505
      featureBiotype: CTCF_binding_site
      dbsnpId: "1"
      variantClass: SNV
      minimised: "1"
  alleleCounts:
    - byPopulation:
        - population: afr
          counts:
            overall:
              an: 5224
            xx:
              an: 2998
            xy:
              an: 2226
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 10882
            xx:
              an: 5942
            xy:
              an: 4940
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 1506
            xx:
              an: 842
            xy:
              an: 664
        - population: eas
          counts:
            overall:
              an: 7858
            xx:
              an: 3798
            xy:
              an: 4060
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts:
            overall:
              an: 5990
        - population: eas_kor
          counts:
            overall:
              an: 1868
        - population: fin
          counts:
            overall:
              an: 732
            xx:
              an: 350
            xy:
              an: 382
        - population: nfe
          counts:
            overall:
              an: 20660
            xx:
              an: 10040
            xy:
              an: 10620
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 4
        - population: nfe_est
          counts:
            overall:
              an: 58
        - population: nfe_nwe
          counts:
            overall:
              an: 16524
        - population: nfe_onf
          counts:
            overall:
              an: 4024
        - population: nfe_seu
          counts:
            overall:
              an: 46
        - population: nfe_swe
          counts:
            overall:
              an: 4
        - population: oth
          counts:
            overall:
              an: 1922
            xx:
              an: 932
            xy:
              an: 990
        - population: sas
          counts:
            overall:
              ac: 4
              an: 6086
              af: 0.000657246
            xx:
              an: 2388
            xy:
              ac: 4
              an: 3698
              af: 0.00108167
          faf95: 0.00022377
          faf99: 0.00022383
      bySex:
        overall:
          ac: 4
          an: 54870
          af: 0.0000728996
        xx:
          an: 27290
        xy:
          ac: 4
          an: 27580
          af: 0.000145033
      raw:
        ac: 4
        an: 105176
        af: 0.0000380315
      popmax: sas
      afPopmax: 0.000657246
      acPopmax: 4
      anPopmax: 6086
      nhomaltPopmax: 0
    - cohort: controls
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 2242
            xx:
              an: 1298
            xy:
              an: 944
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 5530
            xx:
              an: 3116
            xy:
              an: 2414
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 276
            xx:
              an: 124
            xy:
              an: 152
        - population: eas
          counts:
            overall:
              an: 3874
            xx:
              an: 1948
            xy:
              an: 1926
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts:
            overall:
              an: 2946
        - population: eas_kor
          counts:
            overall:
              an: 928
        - population: fin
          counts:
            overall:
              an: 26
            xx:
              an: 14
            xy:
              an: 12
        - population: nfe
          counts:
            overall:
              an: 7114
            xx:
              an: 3750
            xy:
              an: 3364
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts: {}
        - population: nfe_est
          counts:
            overall:
              an: 20
        - population: nfe_nwe
          counts:
            overall:
              an: 5864
        - population: nfe_onf
          counts:
            overall:
              an: 1230
        - population: nfe_seu
          counts: {}
        - population: nfe_swe
          counts: {}
        - population: oth
          counts:
            overall:
              an: 702
            xx:
              an: 360
            xy:
              an: 342
        - population: sas
          counts:
            overall:
              ac: 1
              an: 2804
              af: 0.000356633
            xx:
              an: 1108
            xy:
              ac: 1
              an: 1696
              af: 0.000589623
          faf95: 0.00022377
          faf99: 0.00022383
      bySex:
        overall:
          ac: 1
          an: 22568
          af: 0.0000443105
        xx:
          an: 11718
        xy:
          ac: 1
          an: 10850
          af: 0.0000921659
      raw:
        ac: 1
        an: 42382
        af: 0.0000235949
      popmax: sas
      afPopmax: 0.000356633
      acPopmax: 1
      anPopmax: 2804
      nhomaltPopmax: 0
    - cohort: non_cancer
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 5224
            xx:
              an: 2998
            xy:
              an: 2226
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 10882
            xx:
              an: 5942
            xy:
              an: 4940
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 1506
            xx:
              an: 842
            xy:
              an: 664
        - population: eas
          counts:
            overall:
              an: 7858
            xx:
              an: 3798
            xy:
              an: 4060
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts:
            overall:
              an: 5990
        - population: eas_kor
          counts:
            overall:
              an: 1868
        - population: fin
          counts:
            overall:
              an: 732
            xx:
              an: 350
            xy:
              an: 382
        - population: nfe
          counts:
            overall:
              an: 20660
            xx:
              an: 10040
            xy:
              an: 10620
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 4
        - population: nfe_est
          counts:
            overall:
              an: 58
        - population: nfe_nwe
          counts:
            overall:
              an: 16524
        - population: nfe_onf
          counts:
            overall:
              an: 4024
        - population: nfe_seu
          counts:
            overall:
              an: 46
        - population: nfe_swe
          counts:
            overall:
              an: 4
        - population: oth
          counts:
            overall:
              an: 1922
            xx:
              an: 932
            xy:
              an: 990
        - population: sas
          counts:
            overall:
              ac: 4
              an: 6086
              af: 0.000657246
            xx:
              an: 2388
            xy:
              ac: 4
              an: 3698
              af: 0.00108167
          faf95: 0.00022377
          faf99: 0.00022383
      bySex:
        overall:
          ac: 4
          an: 54870
          af: 0.0000728996
        xx:
          an: 27290
        xy:
          ac: 4
          an: 27580
          af: 0.000145033
      raw:
        ac: 4
        an: 104932
        af: 0.0000381199
      popmax: sas
      afPopmax: 0.000657246
      acPopmax: 4
      anPopmax: 6086
      nhomaltPopmax: 0
    - cohort: non_neuro
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 5192
            xx:
              an: 2984
            xy:
              an: 2208
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 7626
            xx:
              an: 4234
            xy:
              an: 3392
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 654
            xx:
              an: 294
            xy:
              an: 360
        - population: eas
          counts:
            overall:
              an: 7846
            xx:
              an: 3790
            xy:
              an: 4056
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts:
            overall:
              an: 5980
        - population: eas_kor
          counts:
            overall:
              an: 1866
        - population: fin
          counts:
            overall:
              an: 500
            xx:
              an: 186
            xy:
              an: 314
        - population: nfe
          counts:
            overall:
              an: 16902
            xx:
              an: 8748
            xy:
              an: 8154
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 4
        - population: nfe_est
          counts:
            overall:
              an: 50
        - population: nfe_nwe
          counts:
            overall:
              an: 13448
        - population: nfe_onf
          counts:
            overall:
              an: 3394
        - population: nfe_seu
          counts:
            overall:
              an: 2
        - population: nfe_swe
          counts:
            overall:
              an: 4
        - population: oth
          counts:
            overall:
              an: 1536
            xx:
              an: 790
            xy:
              an: 746
        - population: sas
          counts:
            overall:
              ac: 4
              an: 6084
              af: 0.000657462
            xx:
              an: 2388
            xy:
              ac: 4
              an: 3696
              af: 0.00108225
          faf95: 0.00022377
          faf99: 0.00022383
      bySex:
        overall:
          ac: 4
          an: 46340
          af: 0.0000863185
        xx:
          an: 23414
        xy:
          ac: 4
          an: 22926
          af: 0.000174474
      raw:
        ac: 4
        an: 89150
        af: 0.0000448682
      popmax: sas
      afPopmax: 0.000657462
      acPopmax: 4
      anPopmax: 6084
      nhomaltPopmax: 0
    - cohort: non_topmed
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 5074
            xx:
              an: 2900
            xy:
              an: 2174
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 10844
            xx:
              an: 5920
            xy:
              an: 4924
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 1478
            xx:
              an: 828
            xy:
              an: 650
        - population: eas
          counts:
            overall:
              an: 7856
            xx:
              an: 3798
            xy:
              an: 4058
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts:
            overall:
              an: 5988
        - population: eas_kor
          counts:
            overall:
              an: 1868
        - population: fin
          counts:
            overall:
              an: 730
            xx:
              an: 348
            xy:
              an: 382
        - population: nfe
          counts:
            overall:
              an: 19652
            xx:
              an: 9496
            xy:
              an: 10156
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 4
        - population: nfe_est
          counts:
            overall:
              an: 54
        - population: nfe_nwe
          counts:
            overall:
              an: 15814
        - population: nfe_onf
          counts:
            overall:
              an: 3730
        - population: nfe_seu
          counts:
            overall:
              an: 46
        - population: nfe_swe
          counts:
            overall:
              an: 4
        - population: oth
          counts:
            overall:
              an: 1878
            xx:
              an: 908
            xy:
              an: 970
        - population: sas
          counts:
            overall:
              ac: 4
              an: 6086
              af: 0.000657246
            xx:
              an: 2388
            xy:
              ac: 4
              an: 3698
              af: 0.00108167
          faf95: 0.00022377
          faf99: 0.00022383
      bySex:
        overall:
          ac: 4
          an: 53598
          af: 0.0000746297
        xx:
          an: 26586
        xy:
          ac: 4
          an: 27012
          af: 0.000148082
      raw:
        ac: 4
        an: 103858
        af: 0.0000385141
      popmax: sas
      afPopmax: 0.000657246
      acPopmax: 4
      anPopmax: 6086
      nhomaltPopmax: 0
  liftoverInfo:
    originalContig: "1"
    originalStart: "138653"
  rfInfo:
    rfTpProbability: 0.561271
  variantInfo:
    variantType: multi-snv
    alleleType: snv
    nAltAlleles: 3
  qualityInfo:
    fs: 2.105
    inbreedingCoeff: 0.0985
    mq: 36.33
    mqRankSum: -0.376
    qd: 8.31
    readPosRankSum: 0.84
    baseQRankSum: 1.04
    clippingRankSum: 0.374
    sor: 0.908
    dp: 4939758
    vqslod: 0.796
    vqsrCulprit: MQ
    segdup: true
    pabMax: 0.0423948
  ageInfo:
    ageHistHomNSmaller: 0
    ageHistHomNLarger: 0
    ageHistHetNSmaller: 0
    ageHistHetNLarger: 0
  depthInfo:
    dpHistAllNLarger: 15029
    dpHistAltNLarger: 4
- chrom: chr1
  pos: 138654
  refAllele: C
  altAllele: T
  vep:
    - allele: T
      consequence: missense_variant
      impact: MODERATE
      symbol: AL627309.1
      gene: ENSG00000237683
      featureType: Transcript
      feature: ENST00000423372
      featureBiotype: protein_coding
      exon: 1/2
      hgvsc: "ENST00000423372.3:c.656G>A"
      hgvsp: "ENSP00000473460.1:p.Gly219Glu"
      cdnaPosition: "726"
      cdsPosition: "656"
      proteinPosition: "219"
      aminoAcids: G/E
      codons: gGg/gAg
      dbsnpId: "1"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: Clone_based_ensembl_gene
      canonical: true
      ensp: ENSP00000473460
      trembl: R4GN28&B7Z7W4
      uniparc: UPI0002C88512
      sift:
        prediction: deleterious
        score: 0.03
      polyphen:
        prediction: benign
        score: 0.057
    - allele: T
      consequence: downstream_gene_variant
      impact: MODIFIER
      symbol: CICP27
      gene: ENSG00000233750
      featureType: Transcript
      feature: ENST00000442987
      featureBiotype: processed_pseudogene
      dbsnpId: "1"
      distance: "3818"
      strand: "1"
      variantClass: SNV
      minimised: "1"
      symbolSource: HGNC
      hgncId: "48835"
      canonical: true
    - allele: T
      consequence: downstream_gene_variant
      impact: MODIFIER
      symbol: RP11-34P13.13
      gene: ENSG00000241860
      featureType: Transcript
      feature: ENST00000484859
      featureBiotype: antisense
      dbsnpId: "1"
      distance: "2820"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: Clone_based_vega_gene
      canonical: true
    - allele: T
      consequence: downstream_gene_variant
      impact: MODIFIER
      symbol: RP11-34P13.13
      gene: ENSG00000241860
      featureType: Transcript
      feature: ENST00000490997
      featureBiotype: antisense
      dbsnpId: "1"
      distance: "4154"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: Clone_based_vega_gene
    - allele: T
      consequence: downstream_gene_variant
      impact: MODIFIER
      symbol: RP11-34P13.14
      gene: ENSG00000239906
      featureType: Transcript
      feature: ENST00000493797
      featureBiotype: antisense
      dbsnpId: "1"
      distance: "1136"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: Clone_based_vega_gene
      canonical: true
    - allele: T
      consequence: upstream_gene_variant
      impact: MODIFIER
      symbol: RP11-34P13.15
      gene: ENSG00000268903
      featureType: Transcript
      feature: ENST00000494149
      featureBiotype: processed_pseudogene
      dbsnpId: "1"
      distance: "2759"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: Clone_based_vega_gene
      canonical: true
    - allele: T
      consequence: upstream_gene_variant
      impact: MODIFIER
      symbol: RP11-34P13.16
      gene: ENSG00000269981
      featureType: Transcript
      feature: ENST00000595919
      featureBiotype: processed_pseudogene
      dbsnpId: "1"
      distance: "689"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: Clone_based_vega_gene
      canonical: true
    - allele: T
      consequence: regulatory_region_variant
      impact: MODIFIER
      featureType: RegulatoryFeature
      feature: ENSR00000668505
      featureBiotype: CTCF_binding_site
      dbsnpId: "1"
      variantClass: SNV
      minimised: "1"
  alleleCounts:
    - byPopulation:
        - population: afr
          counts:
            overall:
              an: 5224
            xx:
              an: 2998
            xy:
              an: 2226
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              ac: 2
              an: 10890
              af: 0.000183655
            xx:
              ac: 1
              an: 5948
              af: 0.000168124
            xy:
              ac: 1
              an: 4942
              af: 0.000202347
          faf95: 0.00003227
          faf99: 0.0000323
        - population: asj
          counts:
            overall:
              an: 1508
            xx:
              an: 844
            xy:
              an: 664
        - population: eas
          counts:
            overall:
              an: 7858
            xx:
              an: 3798
            xy:
              an: 4060
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts:
            overall:
              an: 5990
        - population: eas_kor
          counts:
            overall:
              an: 1868
        - population: fin
          counts:
            overall:
              an: 732
            xx:
              an: 352
            xy:
              an: 380
        - population: nfe
          counts:
            overall:
              an: 20686
            xx:
              an: 10050
            xy:
              an: 10636
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 4
        - population: nfe_est
          counts:
            overall:
              an: 58
        - population: nfe_nwe
          counts:
            overall:
              an: 16544
        - population: nfe_onf
          counts:
            overall:
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        - population: nfe_seu
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            overall:
              an: 48
        - population: nfe_swe
          counts:
            overall:
              an: 2
        - population: oth
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            overall:
              an: 1920
            xx:
              an: 930
            xy:
              an: 990
        - population: sas
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              an: 6084
            xx:
              an: 2390
            xy:
              an: 3694
          faf95: 0
          faf99: 0
      bySex:
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          af: 0.0000364285
        xx:
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          an: 27310
          af: 0.0000366166
        xy:
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          an: 27592
          af: 0.0000362424
      raw:
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        an: 105366
        af: 0.0000284722
      popmax: amr
      afPopmax: 0.000183655
      acPopmax: 2
      anPopmax: 10890
      nhomaltPopmax: 0
    - cohort: controls
      byPopulation:
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            overall:
              an: 2242
            xx:
              an: 1298
            xy:
              an: 944
          faf95: 0
          faf99: 0
        - population: amr
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              an: 5538
            xx:
              an: 3126
            xy:
              an: 2412
          faf95: 0.00003227
          faf99: 0.0000323
        - population: asj
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            overall:
              an: 276
            xx:
              an: 124
            xy:
              an: 152
        - population: eas
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              an: 3874
            xx:
              an: 1948
            xy:
              an: 1926
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
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            overall:
              an: 2946
        - population: eas_kor
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              an: 928
        - population: fin
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            overall:
              an: 26
            xx:
              an: 14
            xy:
              an: 12
        - population: nfe
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              an: 7122
            xx:
              an: 3754
            xy:
              an: 3368
          faf95: 0
          faf99: 0
        - population: nfe_bgr
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        - population: nfe_est
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            overall:
              an: 20
        - population: nfe_nwe
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            overall:
              an: 5868
        - population: nfe_onf
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              an: 1234
        - population: nfe_seu
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        - population: nfe_swe
          counts: {}
        - population: oth
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              an: 700
            xx:
              an: 358
            xy:
              an: 342
        - population: sas
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            xx:
              an: 1110
            xy:
              an: 1694
          faf95: 0
          faf99: 0
      bySex:
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        xx:
          an: 11732
        xy:
          an: 10850
      raw:
        an: 42482
    - cohort: non_cancer
      byPopulation:
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            xx:
              an: 2998
            xy:
              an: 2226
          faf95: 0
          faf99: 0
        - population: amr
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              an: 10890
              af: 0.000183655
            xx:
              ac: 1
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              af: 0.000168124
            xy:
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              an: 4942
              af: 0.000202347
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        - population: asj
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            xx:
              an: 844
            xy:
              an: 664
        - population: eas
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            xx:
              an: 3798
            xy:
              an: 4060
          faf95: 0
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        - population: eas_jpn
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        - population: eas_oea
          counts:
            overall:
              an: 5990
        - population: eas_kor
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            overall:
              an: 1868
        - population: fin
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            xx:
              an: 352
            xy:
              an: 380
        - population: nfe
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              an: 20686
            xx:
              an: 10050
            xy:
              an: 10636
          faf95: 0
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        - population: nfe_bgr
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        - population: nfe_est
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        - population: nfe_nwe
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        - population: nfe_onf
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        - population: nfe_seu
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        - population: nfe_swe
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        - population: oth
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            xx:
              an: 930
            xy:
              an: 990
        - population: sas
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            xx:
              an: 2390
            xy:
              an: 3694
          faf95: 0
          faf99: 0
      bySex:
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          af: 0.0000364285
        xx:
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          af: 0.0000366166
        xy:
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      raw:
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        af: 0.000028541
      popmax: amr
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      acPopmax: 2
      anPopmax: 10890
      nhomaltPopmax: 0
    - cohort: non_neuro
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            xx:
              an: 2984
            xy:
              an: 2208
          faf95: 0
          faf99: 0
        - population: amr
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              af: 0.000130959
            xx:
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              af: 0.000235738
            xy:
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        - population: asj
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            xx:
              an: 296
            xy:
              an: 360
        - population: eas
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              an: 7846
            xx:
              an: 3790
            xy:
              an: 4056
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
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            overall:
              an: 5980
        - population: eas_kor
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            overall:
              an: 1866
        - population: fin
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            overall:
              an: 500
            xx:
              an: 188
            xy:
              an: 312
        - population: nfe
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            xx:
              an: 8754
            xy:
              an: 8164
          faf95: 0
          faf99: 0
        - population: nfe_bgr
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            overall:
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        - population: nfe_est
          counts:
            overall:
              an: 50
        - population: nfe_nwe
          counts:
            overall:
              an: 13466
        - population: nfe_onf
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            overall:
              an: 3394
        - population: nfe_seu
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            overall:
              an: 2
        - population: nfe_swe
          counts:
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        - population: oth
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            xx:
              an: 788
            xy:
              an: 746
        - population: sas
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            xx:
              an: 2390
            xy:
              an: 3692
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          faf99: 0
      bySex:
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        xx:
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        xy:
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        af: 0.0000223929
      popmax: amr
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      nhomaltPopmax: 0
    - cohort: non_topmed
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        - population: afr
          counts:
            overall:
              an: 5074
            xx:
              an: 2900
            xy:
              an: 2174
          faf95: 0
          faf99: 0
        - population: amr
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            xx:
              ac: 1
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              af: 0.000168748
            xy:
              ac: 1
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        - population: asj
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            xx:
              an: 830
            xy:
              an: 650
        - population: eas
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              an: 7856
            xx:
              an: 3798
            xy:
              an: 4058
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts:
            overall:
              an: 5988
        - population: eas_kor
          counts:
            overall:
              an: 1868
        - population: fin
          counts:
            overall:
              an: 730
            xx:
              an: 350
            xy:
              an: 380
        - population: nfe
          counts:
            overall:
              an: 19678
            xx:
              an: 9506
            xy:
              an: 10172
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 4
        - population: nfe_est
          counts:
            overall:
              an: 54
        - population: nfe_nwe
          counts:
            overall:
              an: 15834
        - population: nfe_onf
          counts:
            overall:
              an: 3736
        - population: nfe_seu
          counts:
            overall:
              an: 48
        - population: nfe_swe
          counts:
            overall:
              an: 2
        - population: oth
          counts:
            overall:
              an: 1876
            xx:
              an: 906
            xy:
              an: 970
        - population: sas
          counts:
            overall:
              an: 6084
            xx:
              an: 2390
            xy:
              an: 3694
          faf95: 0
          faf99: 0
      bySex:
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        xx:
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          af: 0.0000375855
        xy:
          ac: 1
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          af: 0.0000370041
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        af: 0.0000288323
      popmax: amr
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  liftoverInfo:
    originalContig: "1"
    originalStart: "138654"
  rfInfo:
    rfTpProbability: 0.0797253
  variantInfo:
    variantType: snv
    alleleType: snv
    nAltAlleles: 1
  qualityInfo:
    fs: 0.508
    inbreedingCoeff: -0.0431
    mq: 36.86
    mqRankSum: 0.482
    qd: 5.59
    readPosRankSum: 0.516
    baseQRankSum: 3.84
    clippingRankSum: -0.328
    sor: 0.638
    dp: 4938132
    vqslod: 0.585
    vqsrCulprit: QD
    segdup: true
    pabMax: 1
  ageInfo:
    ageHistHomNSmaller: 0
    ageHistHomNLarger: 0
    ageHistHetNSmaller: 0
    ageHistHetNLarger: 0
  depthInfo:
    dpHistAllNLarger: 15028
    dpHistAltNLarger: 2
- chrom: chr1
  pos: 138667
  refAllele: G
  altAllele: C
  vep:
    - allele: C
      consequence: missense_variant
      impact: MODERATE
      symbol: AL627309.1
      gene: ENSG00000237683
      featureType: Transcript
      feature: ENST00000423372
      featureBiotype: protein_coding
      exon: 1/2
      hgvsc: "ENST00000423372.3:c.643C>G"
      hgvsp: "ENSP00000473460.1:p.Leu215Val"
      cdnaPosition: "713"
      cdsPosition: "643"
      proteinPosition: "215"
      aminoAcids: L/V
      codons: Ctt/Gtt
      dbsnpId: "1"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: Clone_based_ensembl_gene
      canonical: true
      ensp: ENSP00000473460
      trembl: R4GN28&B7Z7W4
      uniparc: UPI0002C88512
      sift:
        prediction: tolerated
        score: 0.09
      polyphen:
        prediction: possibly_damaging
        score: 0.801
    - allele: C
      consequence: downstream_gene_variant
      impact: MODIFIER
      symbol: CICP27
      gene: ENSG00000233750
      featureType: Transcript
      feature: ENST00000442987
      featureBiotype: processed_pseudogene
      dbsnpId: "1"
      distance: "3831"
      strand: "1"
      variantClass: SNV
      minimised: "1"
      symbolSource: HGNC
      hgncId: "48835"
      canonical: true
    - allele: C
      consequence: downstream_gene_variant
      impact: MODIFIER
      symbol: RP11-34P13.13
      gene: ENSG00000241860
      featureType: Transcript
      feature: ENST00000484859
      featureBiotype: antisense
      dbsnpId: "1"
      distance: "2807"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: Clone_based_vega_gene
      canonical: true
    - allele: C
      consequence: downstream_gene_variant
      impact: MODIFIER
      symbol: RP11-34P13.13
      gene: ENSG00000241860
      featureType: Transcript
      feature: ENST00000490997
      featureBiotype: antisense
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      distance: "4141"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: Clone_based_vega_gene
    - allele: C
      consequence: downstream_gene_variant
      impact: MODIFIER
      symbol: RP11-34P13.14
      gene: ENSG00000239906
      featureType: Transcript
      feature: ENST00000493797
      featureBiotype: antisense
      dbsnpId: "1"
      distance: "1123"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: Clone_based_vega_gene
      canonical: true
    - allele: C
      consequence: upstream_gene_variant
      impact: MODIFIER
      symbol: RP11-34P13.15
      gene: ENSG00000268903
      featureType: Transcript
      feature: ENST00000494149
      featureBiotype: processed_pseudogene
      dbsnpId: "1"
      distance: "2772"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: Clone_based_vega_gene
      canonical: true
    - allele: C
      consequence: upstream_gene_variant
      impact: MODIFIER
      symbol: RP11-34P13.16
      gene: ENSG00000269981
      featureType: Transcript
      feature: ENST00000595919
      featureBiotype: processed_pseudogene
      dbsnpId: "1"
      distance: "702"
      strand: "-1"
      variantClass: SNV
      minimised: "1"
      symbolSource: Clone_based_vega_gene
      canonical: true
    - allele: C
      consequence: regulatory_region_variant
      impact: MODIFIER
      featureType: RegulatoryFeature
      feature: ENSR00000668505
      featureBiotype: CTCF_binding_site
      dbsnpId: "1"
      variantClass: SNV
      minimised: "1"
  alleleCounts:
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            xx:
              an: 2998
            xy:
              an: 2230
          faf95: 0
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        - population: amr
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              an: 11078
            xx:
              an: 6056
            xy:
              an: 5022
          faf95: 0
          faf99: 0
        - population: asj
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            overall:
              an: 1536
            xx:
              an: 856
            xy:
              an: 680
        - population: eas
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            overall:
              an: 7900
            xx:
              an: 3826
            xy:
              an: 4074
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts:
            overall:
              an: 6032
        - population: eas_kor
          counts:
            overall:
              an: 1868
        - population: fin
          counts:
            overall:
              an: 744
            xx:
              an: 358
            xy:
              an: 386
        - population: nfe
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            overall:
              an: 21110
            xx:
              an: 10294
            xy:
              an: 10816
          faf95: 0
          faf99: 0
        - population: nfe_bgr
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            overall:
              an: 4
        - population: nfe_est
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            overall:
              an: 58
        - population: nfe_nwe
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            overall:
              an: 16862
        - population: nfe_onf
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            overall:
              an: 4110
        - population: nfe_seu
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            overall:
              an: 66
        - population: nfe_swe
          counts:
            overall:
              an: 10
        - population: oth
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            overall:
              an: 1932
            xx:
              an: 936
            xy:
              an: 996
        - population: sas
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              ac: 1
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              af: 0.000163079
            xx:
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            xy:
              ac: 1
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        xx:
          an: 27724
        xy:
          ac: 1
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        af: 0.00000900868
      popmax: sas
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      nhomaltPopmax: 0
    - cohort: controls
      byPopulation:
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          counts:
            overall:
              an: 2244
            xx:
              an: 1298
            xy:
              an: 946
          faf95: 0
          faf99: 0
        - population: amr
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            overall:
              an: 5638
            xx:
              an: 3180
            xy:
              an: 2458
          faf95: 0
          faf99: 0
        - population: asj
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              an: 278
            xx:
              an: 124
            xy:
              an: 154
        - population: eas
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            overall:
              an: 3872
            xx:
              an: 1948
            xy:
              an: 1924
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
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            overall:
              an: 2944
        - population: eas_kor
          counts:
            overall:
              an: 928
        - population: fin
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            overall:
              an: 26
            xx:
              an: 14
            xy:
              an: 12
        - population: nfe
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            overall:
              an: 7186
            xx:
              an: 3784
            xy:
              an: 3402
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts: {}
        - population: nfe_est
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            overall:
              an: 20
        - population: nfe_nwe
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            overall:
              an: 5910
        - population: nfe_onf
          counts:
            overall:
              an: 1254
        - population: nfe_seu
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        - population: nfe_swe
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            overall:
              an: 2
        - population: oth
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            overall:
              an: 704
            xx:
              an: 362
            xy:
              an: 342
        - population: sas
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            xx:
              an: 1112
            xy:
              an: 1700
          faf95: 0.000008
          faf99: 0.000008
      bySex:
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        xx:
          an: 11822
        xy:
          an: 10938
      raw:
        an: 44536
    - cohort: non_cancer
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          counts:
            overall:
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            xx:
              an: 2998
            xy:
              an: 2230
          faf95: 0
          faf99: 0
        - population: amr
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            xx:
              an: 6056
            xy:
              an: 5022
          faf95: 0
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        - population: asj
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            xx:
              an: 856
            xy:
              an: 680
        - population: eas
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              an: 7900
            xx:
              an: 3826
            xy:
              an: 4074
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
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            overall:
              an: 6032
        - population: eas_kor
          counts:
            overall:
              an: 1868
        - population: fin
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            overall:
              an: 744
            xx:
              an: 358
            xy:
              an: 386
        - population: nfe
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              an: 21110
            xx:
              an: 10294
            xy:
              an: 10816
          faf95: 0
          faf99: 0
        - population: nfe_bgr
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            overall:
              an: 4
        - population: nfe_est
          counts:
            overall:
              an: 58
        - population: nfe_nwe
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            overall:
              an: 16862
        - population: nfe_onf
          counts:
            overall:
              an: 4110
        - population: nfe_seu
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            overall:
              an: 66
        - population: nfe_swe
          counts:
            overall:
              an: 10
        - population: oth
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            overall:
              an: 1932
            xx:
              an: 936
            xy:
              an: 996
        - population: sas
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            xx:
              an: 2400
            xy:
              ac: 1
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              af: 0.000267953
          faf95: 0.000008
          faf99: 0.000008
      bySex:
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          af: 0.0000179662
        xx:
          an: 27724
        xy:
          ac: 1
          an: 27936
          af: 0.0000357961
      raw:
        ac: 1
        an: 110688
        af: 0.0000090344
      popmax: sas
      afPopmax: 0.000163079
      acPopmax: 1
      anPopmax: 6132
      nhomaltPopmax: 0
    - cohort: non_neuro
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 5196
            xx:
              an: 2984
            xy:
              an: 2212
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 7820
            xx:
              an: 4346
            xy:
              an: 3474
          faf95: 0
          faf99: 0
        - population: asj
          counts:
            overall:
              an: 662
            xx:
              an: 298
            xy:
              an: 364
        - population: eas
          counts:
            overall:
              an: 7848
            xx:
              an: 3790
            xy:
              an: 4058
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts:
            overall:
              an: 5982
        - population: eas_kor
          counts:
            overall:
              an: 1866
        - population: fin
          counts:
            overall:
              an: 514
            xx:
              an: 196
            xy:
              an: 318
        - population: nfe
          counts:
            overall:
              an: 17284
            xx:
              an: 8982
            xy:
              an: 8302
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 4
        - population: nfe_est
          counts:
            overall:
              an: 50
        - population: nfe_nwe
          counts:
            overall:
              an: 13772
        - population: nfe_onf
          counts:
            overall:
              an: 3446
        - population: nfe_seu
          counts:
            overall:
              an: 2
        - population: nfe_swe
          counts:
            overall:
              an: 10
        - population: oth
          counts:
            overall:
              an: 1544
            xx:
              an: 794
            xy:
              an: 750
        - population: sas
          counts:
            overall:
              ac: 1
              an: 6130
              af: 0.000163132
            xx:
              an: 2400
            xy:
              ac: 1
              an: 3730
              af: 0.000268097
          faf95: 0.000008
          faf99: 0.000008
      bySex:
        overall:
          ac: 1
          an: 46998
          af: 0.0000212775
        xx:
          an: 23790
        xy:
          ac: 1
          an: 23208
          af: 0.0000430886
      raw:
        ac: 1
        an: 93968
        af: 0.0000106419
      popmax: sas
      afPopmax: 0.000163132
      acPopmax: 1
      anPopmax: 6130
      nhomaltPopmax: 0
    - cohort: non_topmed
      byPopulation:
        - population: afr
          counts:
            overall:
              an: 5078
            xx:
              an: 2900
            xy:
              an: 2178
          faf95: 0
          faf99: 0
        - population: amr
          counts:
            overall:
              an: 11040
            xx:
              an: 6034
            xy:
              an: 5006
          faf95: 0
          faf99: 0
        - population: asj
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            overall:
              an: 1508
            xx:
              an: 842
            xy:
              an: 666
        - population: eas
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              an: 7898
            xx:
              an: 3826
            xy:
              an: 4072
          faf95: 0
          faf99: 0
        - population: eas_jpn
          counts: {}
        - population: eas_oea
          counts:
            overall:
              an: 6030
        - population: eas_kor
          counts:
            overall:
              an: 1868
        - population: fin
          counts:
            overall:
              an: 742
            xx:
              an: 356
            xy:
              an: 386
        - population: nfe
          counts:
            overall:
              an: 20102
            xx:
              an: 9750
            xy:
              an: 10352
          faf95: 0
          faf99: 0
        - population: nfe_bgr
          counts:
            overall:
              an: 4
        - population: nfe_est
          counts:
            overall:
              an: 54
        - population: nfe_nwe
          counts:
            overall:
              an: 16152
        - population: nfe_onf
          counts:
            overall:
              an: 3816
        - population: nfe_seu
          counts:
            overall:
              an: 66
        - population: nfe_swe
          counts:
            overall:
              an: 10
        - population: oth
          counts:
            overall:
              an: 1886
            xx:
              an: 910
            xy:
              an: 976
        - population: sas
          counts:
            overall:
              ac: 1
              an: 6132
              af: 0.000163079
            xx:
              an: 2400
            xy:
              ac: 1
              an: 3732
              af: 0.000267953
          faf95: 0.000008
          faf99: 0.000008
      bySex:
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          ac: 1
          an: 54386
          af: 0.0000183871
        xx:
          an: 27018
        xy:
          ac: 1
          an: 27368
          af: 0.000036539
      raw:
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        an: 109674
        af: 0.00000911793
      popmax: sas
      afPopmax: 0.000163079
      acPopmax: 1
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      nhomaltPopmax: 0
  liftoverInfo:
    originalContig: "1"
    originalStart: "138667"
  rfInfo:
    rfTpProbability: 0.0108928
  variantInfo:
    variantType: snv
    alleleType: snv
    nAltAlleles: 1
  qualityInfo:
    fs: 18.822
    inbreedingCoeff: -0.0435
    mq: 34.94
    mqRankSum: -1.023
    qd: 4.06
    readPosRankSum: -0.527
    baseQRankSum: -0.581
    clippingRankSum: 0.03
    sor: 0.09
    dp: 4968225
    vqslod: -13.81
    vqsrCulprit: FS
    segdup: true
    pabMax: 0.000000000185456
  ageInfo:
    ageHistHomNSmaller: 0
    ageHistHomNLarger: 0
    ageHistHetNSmaller: 0
    ageHistHetNLarger: 0
  depthInfo:
    dpHistAllNLarger: 15028
    dpHistAltNLarger: 1

