GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3 (copy change)

This example represents the same ClinVar variant as categoricalCnv-ex1, with all top-level attributes populated identically. The distinction between the two examples lies solely in the constraint applied.

Source

ClinVar variation 151061: GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3

Recipes that this example satisfies

Categorical CNV

Properties

id: clinvar:151061: ClinVar Variation ID, 151061 is the Variation ID listed within the Identifiers section of ClinVar’s Variant Details.
type: CategoricalVariant: This value is required by the specification for all Categorical Variant objects.
name: GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3: Human-readable label listed within the Identifiers section of ClinVar’s Variant Details.
description: An optional field to describe this Categorical Variant.: This field was populated with an example value because ClinVar does not provide a longform description.
aliases: 2 HGVS expressions: All listed HGVS representations within ClinVar’s Variant Details for the variant, including the GRCh38 (NC_000007.14) and GRCh37 (NC_000007.13) genomic representations.
extensions: cytogenetic location, clinvar variation type, and hgvs list: The cytogenetic location (7p22.1) and ClinVar variation type (copy number gain) are obtained from ClinVar’s Variant Details. The hgvs list extension includes the GRCh38 and GRCh37 HGVS genomic representations.
mappings: ClinVar and dbVar: Mappings to ClinVar’s page for the variant and dbVar are included from the Links section of ClinVar’s Variant Details.

Constraints

Copy Change Constraint: The copyChange field is set to gain, matching the copyChange value within the VRS CopyNumberChange objects listed under members. This contrasts with categoricalCnv-ex1, which uses a Copy Count Constraint to specify an exact copy count of 3.
Defining Location Constraint: The defining location is a VRS Sequence Location on chromosome 7 (refseq:NC_000007.14, GRCh38) spanning positions 5,905,831 to 6,014,161, extracted from the GRCh38 CopyNumberChange included within members. The matchCharacteristic is set to is_within, and a liftover relation is included to link the GRCh38 and GRCh37 representations.

Members

The members field includes two VRS CopyNumberChange objects generated using the VICC Variation Normalizer from the HGVS representations of this variant:

NC_000007.14:g.(?_5905831)_(6014161_?)dup (GRCh38)
NC_000007.13:g.(?_5945462)_(6053792_?)dup (GRCh37)

Both members have a copyChange value of gain.

Full example: JSON

{
  "id": "clinvar:151061",
  "type": "CategoricalVariant",
  "name": "GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3 (copy change)",
  "description": "An example categorical CNV that uses CopyChangeConstraint.",
  "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": "CopyChangeConstraint",
      "copyChange": "gain"
    },
    {
      "type": "DefiningLocationConstraint",
      "location": {
        "id": "ga4gh:SL.LChpEzYZaMug85TUqJUbT4MYgVk8vuQ7",
        "name": "NC_000007.14:g.(?_5905831)_(6014161_?)",
        "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": "CopyNumberChange",
      "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 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"
        },
        "start": [
          null,
          5905830
        ],
        "end": [
          6014161,
          null
        ]
      },
      "copyChange": "gain"
    },
    {
      "id": "ga4gh:CX.XfVcSnSqR2oJHzBMueTrgkMWg_UgbuBL",
      "type": "CopyNumberChange",
      "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 5945462 to 6053792 on chromosome 7 (refseq:NC_000007.13, GRCh37).",
        "extensions": [
          {
            "name": "GRCh37 1-based, inclusive interval",
            "value": "chr7:5945462-6053792",
            "description": "Genomic positions 5945462 to 6053792 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 5945461 to 6053792 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
        ]
      },
      "copyChange": "gain"
    }
  ]
}

Full example: YAML

id: clinvar:151061
type: CategoricalVariant
name: GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3 (copy change)
description: An example categorical CNV that uses CopyChangeConstraint.
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: CopyChangeConstraint
    copyChange: gain
  - type: DefiningLocationConstraint
    location:
      id: ga4gh:SL.LChpEzYZaMug85TUqJUbT4MYgVk8vuQ7
      name: NC_000007.14:g.(?_5905831)_(6014161_?)
      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: CopyNumberChange
    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 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
      start:
        - null
        - 5905830
      end:
        - 6014161
        - null
    copyChange: gain
  - id: ga4gh:CX.XfVcSnSqR2oJHzBMueTrgkMWg_UgbuBL
    type: CopyNumberChange
    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 5945462 to 6053792 on chromosome 7 (refseq:NC_000007.13, GRCh37).
      extensions:
        - name: GRCh37 1-based, inclusive interval
          value: chr7:5945462-6053792
          description: Genomic positions 5945462 to 6053792 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 5945461 to 6053792 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
    copyChange: gain