cat-vrs/examples/yaml/canonicalAllele-ex2.yaml at v1 · ga4gh/cat-vrs · GitHub

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id: clingen:CA415424538
type: CategoricalVariant
name: NC_000001.11:g.1699974C>G
description: An example canonical allele.
aliases:
  - NC_000001.11:g.1699974C>G
  - NC_000001.10:g.1631413C>G
extensions:
  - name: cytogenetic location
    value: 1p36.33
  - name: hgvs list
    value:
      - nucleotideExpression:
          syntax: hgvs.g
          value: NC_000001.11:g.1699974C>G
      - nucleotideExpression:
          syntax: hgvs.g
          value: NC_000001.10:g.1631413C>G
constraints:
  - type: DefiningAlleleConstraint
    allele:
      id: ga4gh:VA.WjRY1EXgci6Nd0M2yI86Ue_OOnfnb-Ss
      type: Allele
      name: NC_000001.11:g.1699974C>G
      description: VRS Allele of NC_000001.11:g.1699974C>G, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).
      digest: WjRY1EXgci6Nd0M2yI86Ue_OOnfnb-Ss
      expressions:
        - syntax: hgvs.g
          value: NC_000001.11:g.1699974C>G
      location:
        id: ga4gh:SL.YmbtK6FLqlk2bLjpFwH-y7k4RLq_t7L3
        description: Genomic position 1699974 on chromosome 1 (refseq:NC_000001.11, GRCh38).
        extensions:
          - name: GRCh38 1-based, genomic position
            value: chr1:1699974
            description: Genomic position 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38).
          - name: GRCh38 1-based, inclusive interval notation
            value: chr1:1699974-1699974
            description: Genomic positions 1,699,974 to 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38); 1-based, inclusive interval notation.
          - name: GRCh38 0-based, half-open interval notation
            value: chr1:1699973-1699974
            description: Genomic positions 1,699,973 to 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38); 0-based, half-open interval notation.
        type: SequenceLocation
        digest: YmbtK6FLqlk2bLjpFwH-y7k4RLq_t7L3
        sequenceReference:
          id: refseq:NC_000001.11
          name: NC_000001.11
          description: Reference sequence for GRCh38 chromosome 1.
          aliases:
            - GRCh38:1
            - GRCh38:chr1
            - ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO
          type: SequenceReference
          refgetAccession: SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO
          residueAlphabet: na
        start: 1699973
        end: 1699974
        sequence: C
      state:
        type: LiteralSequenceExpression
        sequence: G
    relations:
      - primaryCoding:
          code: liftover_to
          system: ga4gh-gks-term:allele-relation
      - primaryCoding:
          code: transcribed_to
          system: http://www.sequenceontology.org
          iris:
            - http://www.sequenceontology.org/browser/current_release/term/transcribed_to
mappings:
  - coding:
      system: https://reg.clinicalgenome.org/
      code: CA415424538
      iris:
        - https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA415424538
    relation: exactMatch
  - coding:
      system: https://www.ncbi.nlm.nih.gov/snp/
      code: rs1391950675
      iris:
        - https://www.ncbi.nlm.nih.gov/snp/rs1391950675
    relation: relatedMatch
  - coding:
      system: https://gnomad.broadinstitute.org
      code: 1-1631413-C-G
      iris:
        - https://gnomad.broadinstitute.org/variant/1-1631413-C-G?dataset=gnomad_r2_1
      extensions:
        - name: dataset
          value: gnomad_r2_1
    relation: relatedMatch
  - coding:
      system: https://gnomad.broadinstitute.org
      code: 1-1699974-C-G
      iris:
        - https://gnomad.broadinstitute.org/variant/1-1699974-C-G?dataset=gnomad_r3
      extensions:
        - name: dataset
          value: gnomad_r3
    relation: relatedMatch
  - coding:
      system: https://gnomad.broadinstitute.org
      code: chr1-1699974-C-G
      iris:
        - https://gnomad.broadinstitute.org/variant/chr1-1699974-C-G?dataset=gnomad_r4
      extensions:
        - name: dataset
          value: gnomad_r4
    relation: relatedMatch
members:
  - id: ga4gh:VA.WjRY1EXgci6Nd0M2yI86Ue_OOnfnb-Ss
    type: Allele
    name: NC_000001.11:g.1699974C>G
    description: VRS variation of NC_000001.11:g.1699974C>G, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).
    digest: WjRY1EXgci6Nd0M2yI86Ue_OOnfnb-Ss
    expressions:
      - syntax: hgvs.g
        value: NC_000001.11:g.1699974C>G
    location:
      id: ga4gh:SL.YmbtK6FLqlk2bLjpFwH-y7k4RLq_t7L3
      description: Genomic position 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38).
      type: SequenceLocation
      extensions:
        - name: GRCh38 1-based, genomic position
          value: chr1:1699974
          description: Genomic position 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38).
        - name: GRCh38 1-based, inclusive interval notation
          value: chr1:1699974-1699974
          description: Genomic positions 1,699,974 to 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38); 1-based, inclusive interval notation.
        - name: GRCh38 0-based, half-open interval notation
          value: chr1:1699973-1699974
          description: Genomic positions 1,699,973 to 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38); 0-based, half-open interval notation.
      digest: YmbtK6FLqlk2bLjpFwH-y7k4RLq_t7L3
      sequenceReference:
        id: refseq:NC_000001.11
        name: NC_000001.11
        description: Reference sequence for GRCh38 chromosome 1.
        aliases:
          - GRCh38:1
          - GRCh38:chr1
          - ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO
        type: SequenceReference
        refgetAccession: SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO
        residueAlphabet: na
      start: 1699973
      end: 1699974
      sequence: C
    state:
      type: LiteralSequenceExpression
      sequence: G
  - id: ga4gh:VA.WW0r6Dh-z_ftn9yS-i0f1Y62JNCpVed2
    type: Allele
    name: NC_000001.10:g.1631413C>G
    description: VRS variation of NC_000001.10:g.1631413C>G, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).
    digest: WW0r6Dh-z_ftn9yS-i0f1Y62JNCpVed2
    expressions:
      - syntax: hgvs.g
        value: NC_000001.10:g.1631413C>G
    location:
      id: ga4gh:SL.QsC4TgLsfR6-TatBj1sVKAgfv9bGYSxb
      description: Genomic position 1,631,413 on chromosome 1 (refseq:NC_000001.10, GRCh37).
      type: SequenceLocation
      extensions:
        - name: GRCh37 1-based, genomic position
          value: chr1:1631413
          description: Genomic position 1,631,413 on chromosome 1 (refseq:NC_000001.10, GRCh37).
        - name: GRCh37 1-based, inclusive interval notation
          value: chr1:1631413-1631413
          description: Genomic positions 1,631,413 to 1,631,413 on chromosome 1 (refseq:NC_000001.10, GRCh37); 1-based, inclusive interval notation.
        - name: GRCh37 0-based, half-open interval notation
          value: chr1:1631412-1631413
          description: Genomic positions 1,631,412 to 1,631,413 on chromosome 1 (refseq:NC_000001.10, GRCh37); 0-based, half-open interval notation.
      digest: QsC4TgLsfR6-TatBj1sVKAgfv9bGYSxb
      sequenceReference:
        id: refseq:NC_000001.10
        name: NC_000001.10
        description: Reference sequence for GRCh37 chromosome 1.
        aliases:
          - GRCh37.1
          - GRCh37:chr1
          - ga4gh:SQ.S_KjnFVz-FE7M0W6yoaUDgYxLPc1jyWU
        type: SequenceReference
        refgetAccession: SQ.S_KjnFVz-FE7M0W6yoaUDgYxLPc1jyWU
        residueAlphabet: na
      start: 1631412
      end: 1631413
      sequence: C
    state:
      type: LiteralSequenceExpression
      sequence: G