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

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id: clinvar:55628
type: CategoricalVariant
name: NM_007294.4(BRCA1):c.5558dup (p.Tyr1853Ter)
description: An example categorical variant that models NM_007294.4(BRCA1):c.5558dup (p.Tyr1853Ter) from ClinVar.
aliases:
  - NM_007294.4:c.5558dup
  - NP_009225.1:p.Tyr1853Ter
  - NP_009225.1:p.Y1853*
  - NM_007294.4(BRCA1):c.5558dup (p.Y1853*)
  - NC_000017.11:g.43045712dup
  - NC_000017.10:g.41197729dup
  - NC_000017.11:43045711:T:TT
extensions:
  - name: cytogenetic location
    value: 17q21.31
  - name: clinvar variation type
    value: Duplication
  - name: hgvs list
    value:
      - nucleotideExpression:
          syntax: hgvs.g
          value: NC_000017.11:g.43045712dup
        nucleotideType: genomic
      - nucleotideExpression:
          syntax: hgvs.g
          value: NC_000017.10:g.41197729dup
        nucleotideType: genomic
      - nucleotideExpression:
          syntax: hgvs.c
          value: NM_007294.4:c.5558dup
        nucleotideType: coding
        maneSelect: true
        proteinExpression:
          syntax: hgvs.p
          value: NP_009225.1:p.Tyr1853Ter
        molecularConsequence:
          name: stop_gained
          system: http://www.sequenceontology.org/browser/
          systemVersion: release_2.5.3
          code: SO:0001587
          iris:
            - http://www.sequenceontology.org/browser/release_2.5.3/term/SO:0001587
constraints:
  - type: DefiningAlleleConstraint
    allele:
      id: ga4gh:VA.BfZ-RbjStWkafMsFBcoSL0f4aAjHJU4n
      type: Allele
      name: NP_009225.1:p.Tyr1853Ter
      description: VRS variation of NP_009225.1:p.Tyr1853Ter, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).
      digest: BfZ-RbjStWkafMsFBcoSL0f4aAjHJU4n
      expressions:
        - syntax: hgvs.g
          value: NC_000017.11:g.43045712dup
        - syntax: hgvs.g
          value: NC_000017.10:g.41197729dup
        - syntax: hgvs.c
          value: NM_007294.4:c.5558dup
        - syntax: hgvs.p
          value: NP_009225.1:p.Tyr1853Ter
      location:
        id: ga4gh:SL.bR3EOtSngkb9wNbixylsw0sNa_2HCga5
        description: Amino acid position 1853 of the Refseq protein NP_009225.1, which is the protein product of the MANE Select (GRCh38) coding transcript for BRCA1 (refseq:NM_007294.4).
        type: SequenceLocation
        digest: bR3EOtSngkb9wNbixylsw0sNa_2HCga5
        sequenceReference:
          id: refseq:NP_009225.1
          name: NP_009225.1
          description: The protein product of the MANE Select (GRCh38) coding transcript for BRCA1 (refseq:NM_007294.4), corresponding to the Refseq protein accession NP_009225.1.
          aliases:
            - ensembl:ENSP00000350283.3
            - ga4gh:SQ.nUzIPnHMyQV52hzgBbKl5vlbSwx8M8_Y
          type: SequenceReference
          refgetAccession: SQ.nUzIPnHMyQV52hzgBbKl5vlbSwx8M8_Y
          residueAlphabet: aa
        start: 1852
        end: 1853
        sequence: Y
      state:
        type: LiteralSequenceExpression
        sequence: '*'
    relations:
      - primaryCoding:
          code: translation_of
          system: http://www.sequenceontology.org
          iris:
            - http://www.sequenceontology.org/browser/current_release/term/translation_of
mappings:
  - coding:
      system: https://www.ncbi.nlm.nih.gov/clinvar
      code: '55628'
      iris:
        - https://www.ncbi.nlm.nih.gov/clinvar/variation/55628/
    relation: exactMatch
  - coding:
      system: https://reg.clinicalgenome.org/
      code: CA003713
      iris:
        - https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA003713
    relation: relatedMatch
  - coding:
      system: https://www.ncbi.nlm.nih.gov/snp
      code: rs80357629
      iris:
        - https://www.ncbi.nlm.nih.gov/snp/rs80357629
    relation: relatedMatch
members:
  - id: ga4gh:VA.ju31SHNY7xeTI244BcOS7J78dIek46xL
    type: Allele
    name: NC_000017.11:g.43045712dup
    description: VRS variation of NC_000017.11:g.43045712dup, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).
    digest: ju31SHNY7xeTI244BcOS7J78dIek46xL
    expressions:
      - syntax: hgvs.g
        value: NC_000017.11:g.43045712dup
      - syntax: hgvs.g
        value: NC_000017.10:g.41197729dup
      - syntax: hgvs.c
        value: NM_007294.4:c.5558dup
      - syntax: hgvs.p
        value: NP_009225.1:p.Tyr1853Ter
    location:
      id: ga4gh:SL.El1CbTY3p0rvxxkf5qI3YdgTo46YIjwl
      description: Genomic position 43,045,712 on chromosome 17 (refseq:NC_000017.11, GRCh38).
      type: SequenceLocation
      extensions:
        - name: GRCh38 1-based, genomic position
          value: chr17:43045712
          description: Genomic position 43,045,712 on chromosome 17 (refseq:NC_000017.11, GRCh38).
        - name: GRCh38 1-based, inclusive interval notation
          value: chr17:43045712-43045712
          description: Genomic positions 43,045,712 to 43,045,712 on chromosome 17 (refseq:NC_000017.11, GRCh38); 1-based, inclusive interval notation.
        - name: GRCh38 0-based, half-open interval notation
          value: chr17:43045711-43045712
          description: Genomic positions 43,045,711 to 43,045,712 on chromosome 17 (refseq:NC_000017.11, GRCh38); 0-based, half-open interval notation.
      digest: El1CbTY3p0rvxxkf5qI3YdgTo46YIjwl
      sequenceReference:
        id: refseq:NC_000017.11
        name: NC_000017.11
        description: Reference sequence for GRCh38 chromosome 17
        type: SequenceReference
        refgetAccession: SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7
        residueAlphabet: na
      start: 43045711
      end: 43045712
      sequence: T
    state:
      type: ReferenceLengthExpression
      length: 2
      sequence: TT
      repeatSubunitLength: 1
  - id: ga4gh:VA.UPNFCFuk1_6v7IzYbbQTV_PsYJ9WOwSa
    type: Allele
    name: NC_000017.10:g.41197729dup
    description: VRS variation of NC_000017.10:g.41197729dup, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).
    digest: UPNFCFuk1_6v7IzYbbQTV_PsYJ9WOwSa
    expressions:
      - syntax: hgvs.g
        value: NC_000017.11:g.43045712dup
      - syntax: hgvs.g
        value: NC_000017.10:g.41197729dup
      - syntax: hgvs.c
        value: NM_007294.4:c.5558dup
      - syntax: hgvs.p
        value: NP_009225.1:p.Tyr1853Ter
    location:
      id: ga4gh:SL.bJxQ_soqGHGy4skIMKp6VLEB54XH32M8
      description: Genomic position 41,197,729 on chromosome 17 (refseq:NC_000017.10, GRCh37).
      type: SequenceLocation
      extensions:
        - name: GRCh37 1-based, genomic position
          value: chr17:41197729
          description: Genomic position 41,197,729 on chromosome 17 (refseq:NC_000017.10, GRCh37).
        - name: GRCh37 1-based, inclusive interval notation
          value: chr17:41197729-41197729
          description: Genomic position 41,197,729 to 41,197,729 on chromosome 17 (refseq:NC_000017.10, GRCh37); 1-based, inclusive interval notation.
        - name: GRCh37 0-based, half-open interval notation
          value: chr17:41197728-41197729
          description: Genomic position 41,197,728 to 41,197,729 on chromosome 17 (refseq:NC_000017.10, GRCh37); 0-based, half-open interval notation.
      digest: bJxQ_soqGHGy4skIMKp6VLEB54XH32M8
      sequenceReference:
        id: refseq:NC_000017.10
        name: NC_000017.10
        description: Reference sequence for GRCh37 chromosome 17.
        aliases:
          - GRCh37:17
          - GRCh37:chr17
          - ga4gh:SQ.AjWXsI7AkTK35XW9pgd3UbjpC3MAevlz
        type: SequenceReference
        refgetAccession: SQ.AjWXsI7AkTK35XW9pgd3UbjpC3MAevlz
        residueAlphabet: na
      start: 41197728
      end: 41197729
      sequence: T
    state:
      type: ReferenceLengthExpression
      length: 2
      sequence: TT
      repeatSubunitLength: 1
  - id: ga4gh:VA.BfZ-RbjStWkafMsFBcoSL0f4aAjHJU4n
    type: Allele
    name: NP_009225.1:p.Tyr1853Ter
    description: VRS variation of NP_009225.1:p.Tyr1853Ter, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).
    digest: BfZ-RbjStWkafMsFBcoSL0f4aAjHJU4n
    expressions:
      - syntax: hgvs.g
        value: NC_000017.11:g.43045712dup
      - syntax: hgvs.g
        value: NC_000017.10:g.41197729dup
      - syntax: hgvs.c
        value: NM_007294.4:c.5558dup
      - syntax: hgvs.p
        value: NP_009225.1:p.Tyr1853Ter
    location:
      id: ga4gh:SL.bR3EOtSngkb9wNbixylsw0sNa_2HCga5
      description: Amino acid position 1853 of the Refseq protein NP_009225.1, which is the protein product of the MANE Select (GRCh38) coding transcript for BRCA1 (refseq:NM_007294.4).
      type: SequenceLocation
      digest: bR3EOtSngkb9wNbixylsw0sNa_2HCga5
      sequenceReference:
        id: refseq:NP_009225.1
        name: NP_009225.1
        description: The protein product of the MANE Select (GRCh38) coding transcript for BRCA1 (refseq:NM_007294.4), corresponding to the Refseq protein accession NP_009225.1.
        aliases:
          - ensembl:ENSP00000350283.3
          - ga4gh:SQ.nUzIPnHMyQV52hzgBbKl5vlbSwx8M8_Y
        type: SequenceReference
        refgetAccession: SQ.nUzIPnHMyQV52hzgBbKl5vlbSwx8M8_Y
        residueAlphabet: aa
      start: 1852
      end: 1853
      sequence: Y
    state:
      type: LiteralSequenceExpression
      sequence: '*'