cat-vrs/examples/yaml/categoricalCnv-ex1.yaml at v1 · ga4gh/cat-vrs · GitHub

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id: clinvar:151061
type: CategoricalVariant
name: GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3 (copy count)
description: An example categorical CNV that uses CopyCountConstraint.
aliases:
  - NC_000007.14:g.(?_5905831)_(6014161_?)dup
  - NC_000007.13:g.(?_5945462)_(6053792_?)dup
extensions:
  - name: cytogenetic location
    value: 7p22.1
  - name: clinvar variation type
    value: copy number gain
  - name: hgvs list
    value:
      - nucleotideExpression:
          syntax: hgvs.g
          value: NC_000007.14:g.(?_5905831)_(6014161_?)dup
        nucleotideType: genomic
      - nucleotideExpression:
          syntax: hgvs.g
          value: NC_000007.13:g.(?_5945462)_(6053792_?)dup
        nucleotideType: genomic
constraints:
  - type: CopyCountConstraint
    copies: 3
  - type: DefiningLocationConstraint
    location:
      id: ga4gh:SL.LChpEzYZaMug85TUqJUbT4MYgVk8vuQ7
      description: Genomic positions 5905831 to 6014161 on chromosome 7 (refseq:NC_000007.14, GRCh38).
      extensions:
        - name: GRCh38 1-based, inclusive interval
          value: chr7:5905831-6014161
          description: Genomic positions 5905831 to 6014161 on chromosome 7 (refseq:NC_000007.14, GRCh38); 1-based, inclusive interval notation.
        - name: GRCh38 0-based, half-open interval
          value: chr7:5905830-6014161
          description: Genomic positions 5905830 to 6014161 on chromosome 7 (refseq:NC_000007.14, GRCh38); 0-based, half-open interval notation.
      type: SequenceLocation
      digest: LChpEzYZaMug85TUqJUbT4MYgVk8vuQ7
      sequenceReference:
        id: refseq:NC_000007.14
        name: NC_000007.14
        description: Reference sequence for GRCh38 chromosome 7.
        aliases:
          - GRCh38:7
          - GRCh38:chr7
          - ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul
        type: SequenceReference
        refgetAccession: SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul
        residueAlphabet: na
      start:
        - null
        - 5905830
      end:
        - 6014161
        - null
    relations:
      - primaryCoding:
          code: liftover_to
          system: ga4gh-gks-term:allele-relation
    matchCharacteristic:
      primaryCoding:
        code: is_within
        system: ga4gh-gks-term:location-match
mappings:
  - coding:
      system: https://www.ncbi.nlm.nih.gov/clinvar
      code: '151061'
      iris:
        - https://www.ncbi.nlm.nih.gov/clinvar/variation/151061
    relation: exactMatch
  - coding:
      system: https://www.ncbi.nlm.nih.gov/dbvar
      code: nsv930939
      iris:
        - https://www.ncbi.nlm.nih.gov/dbvar/variants/nssv1610575/
    relation: relatedMatch
members:
  - id: ga4gh:CX.W8HqtDWeVQy_pq6fOSqnPlAcNnH9vvz4
    type: CopyNumberCount
    name: NC_000007.14:g.(?_5905831)_(6014161_?)dup
    description: VRS variation of NC_000007.14:g.(?_5905831)_(6014161_?)dup, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).
    digest: W8HqtDWeVQy_pq6fOSqnPlAcNnH9vvz4
    expressions:
      - syntax: hgvs.g
        value: NC_000007.14:g.(?_5905831)_(6014161_?)dup
    location:
      id: ga4gh:SL.LChpEzYZaMug85TUqJUbT4MYgVk8vuQ7
      description: Genomic positions 5,905,831 to 6,014,161 on chromosome 7 (refseq:NC_000007.14, GRCh38).
      extensions:
        - name: GRCh38 1-based, inclusive interval
          value: chr7:5905831-6014161
          description: Genomic positions 5,905,831 to 6,014,161 on chromosome 7 (refseq:NC_000007.14, GRCh38); 1-based, inclusive interval notation.
        - name: GRCh38 0-based, half-open interval
          value: chr7:5905830-6014161
          description: Genomic positions 5,905,830 to 6,014,161 on chromosome 7 (refseq:NC_000007.14, GRCh38); 0-based, half-open interval notation.
      type: SequenceLocation
      digest: LChpEzYZaMug85TUqJUbT4MYgVk8vuQ7
      sequenceReference:
        id: refseq:NC_000007.14
        name: NC_000007.14
        description: Reference sequence for GRCh38 chromosome 7.
        aliases:
          - GRCh38:7
          - GRCh38:chr7
          - ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul
        type: SequenceReference
        refgetAccession: SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul
      start:
        - null
        - 5905830
      end:
        - 6014161
        - null
    copies: 3
  - id: ga4gh:CX.XfVcSnSqR2oJHzBMueTrgkMWg_UgbuBL
    type: CopyNumberCount
    name: NC_000007.13:g.(?_5945462)_(6053792_?)dup
    description: VRS variation of NC_000007.13:g.(?_5945462)_(6053792_?)dup, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).
    digest: XfVcSnSqR2oJHzBMueTrgkMWg_UgbuBL
    expressions:
      - syntax: hgvs.g
        value: NC_000007.13:g.(?_5945462)_(6053792_?)dup
    location:
      id: ga4gh:SL.9wrSvk5-4mI6CmYrt6vImSzcLssLY3VJ
      description: Genomic positions 5,945,462 to 6,053,792 on chromosome 7 (refseq:NC_000007.13, GRCh37).
      extensions:
        - name: GRCh37 1-based, inclusive interval
          value: chr7:5945462-6053792
          description: Genomic positions 5,945,462 to 6,053,792 on chromosome 7 (refseq:NC_000007.13, GRCh37); 1-based, inclusive interval notation.
        - name: GRCh38 0-based, half-open interval
          value: chr7:5945461-6053792
          description: Genomic positions 5,945,461 to 6,053,792 on chromosome 7 (refseq:NC_000007.13, GRCh37); 0-based, half-open interval notation.
      type: SequenceLocation
      digest: 9wrSvk5-4mI6CmYrt6vImSzcLssLY3VJ
      sequenceReference:
        id: refseq:NC_000007.13
        name: NC_000007.13
        description: Reference sequence for GRCh37 chromosome 7.
        aliases:
          - GRCh37:7
          - GRCh37:chr7
          - ga4gh:SQ.IW78mgV5Cqf6M24hy52hPjyyo5tCCd86
        type: SequenceReference
        refgetAccession: SQ.IW78mgV5Cqf6M24hy52hPjyyo5tCCd86
        residueAlphabet: na
      start:
        - null
        - 5945461
      end:
        - 6053792
        - null
    copies: 3