GRCh38 Xp22.31(chrX:6978350-7594949)x3

Source

ClinGen CACN42032202

Recipes that this example satisfies

Categorical CNV

Properties

id: clingen:cacn42032202: ClinGen Canonical CNV Identifier, where CACN42032202 is provided by ClinGen.
type: CategoricalVariant: This value is required by the specification for all Categorical Variant objects.
name: GRCh38 Xp22.31(chrX:6978350-7594949)x3: The Community Standard Title listed for the variant by ClinGen.
description: An optional field to describe this Categorical Variant.: This field was populated with an example value because ClinGen does not provide a longform description.
aliases: 2 HGVS expressions: The HGVS representations for GRCh38 (NC_000023.11) and GRCh37 (NC_000023.10) are listed.
extensions: cytogenetic location: The cytogenetic location (Xp22.31) was obtained from the Community Standard Title for this variant.
mappings: ClinGen: A mapping to ClinGen’s webpage for this variant is included.

Constraints

Copy Count Constraint: The copies field is set to 3, reflecting the “x3” copy count specified in the variant name as provided by ClinGen.
Defining Location Constraint: The defining location is a VRS Sequence Location on chromosome X (refseq:NC_000023.11, GRCh38), extracted from the GRCh38 CopyNumberCount included within members. Unlike categoricalCnv-ex1 and categoricalCnv-ex2, this example uses ranged values for both the start and end positions to reflect uncertainty in the breakpoint locations, specifying start within the interval 6,978,350–6,996,235 and end within 7,564,455–7,594,949.

Members

The members field includes one VRS CopyNumberCount object generated using the VICC Variation Normalizer: NC_000023.11:g.(6978350_6996235)_(7564455_7594949)dup on the GRCh38 chromosome X reference sequence, with a copies value of 3 and ranged start and end positions reflecting breakpoint uncertainty.

Full example: JSON

{
  "id": "clingen:cacn42032202",
  "type": "CategoricalVariant",
  "name": "GRCh38 Xp22.31(chrX:6978350-7594949)x3",
  "description": "An example categoricalCNV that uses CopyCountConstraint and uses ranges for start/end positions within the DefiningLocationConstraint.",
  "aliases": [
    "NC_000023.11:g.(6978350_6996235)_(7564455_7594949)dup(2)",
    "GRCh37 (chrX:6896391_6914276-7482496_7512990)x3",
    "NC_000023.10:g.(6896391_6914276-7482496_7512990)dup(2)"
  ],
  "extensions": [
    {
      "name": "cytogenetic location",
      "value": "Xp22.31"
    }
  ],
  "constraints": [
    {
      "type": "CopyCountConstraint",
      "copies": 3
    },
    {
      "type": "DefiningLocationConstraint",
      "location": {
        "id": "ga4gh:SL.XyercAFM_APQwFaDuPcXG5lHa4wUpkiL",
        "description": "Genomic region between positions 6,978,350-7,594,949 on chromosome X (refseq:NC_000023.11, GRCh38), with breakpoints estimated within the intervals 6,978,350-6,996,235 and 7,564,455-7,594,949.",
        "extensions": [
          {
            "name": "GRCh38 1-based, inclusive interval",
            "value": "chrX:(6978350\u20136996235)-(7564455\u20137594949)",
            "description": "Genomic region between positions 6,978,350-7,594,949 on chromosome X (refseq:NC_000023.11, GRCh38), with breakpoints estimated within the intervals 6,978,350-6,996,235 and 7,564,455-7,594,949; 1-based, inclusive interval notation."
          },
          {
            "name": "GRCh38 0-based, half-open interval",
            "value": "chrX:(6978349\u20136996235)-(7564454\u20137594949)",
            "description": "Genomic region between positions 6,978,349-7,594,949 on chromosome X (refseq:NC_000023.11, GRCh38), with breakpoints estimated within the intervals 6,978,349-6,996,235 and 7,564,454-7,594,949; 0-based, half-open interval notation."
          }
        ],
        "type": "SequenceLocation",
        "digest": "XyercAFM_APQwFaDuPcXG5lHa4wUpkiL",
        "sequenceReference": {
          "id": "refseq:NC_000023.11",
          "name": "NC_000023.11",
          "description": "Reference sequence for GRCh38 chromosome X.",
          "aliases": [
            "GRCh38:X",
            "GRCh38:chrX",
            "ga4gh:SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP"
          ],
          "type": "SequenceReference",
          "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul"
        },
        "start": [
          6978350,
          6996235
        ],
        "end": [
          7564455,
          7594949
        ]
      },
      "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://reg.clinicalgenome.org/",
        "code": "CACN42032202",
        "iris": [
          "https://reg.clinicalgenome.org/redmine/projects/Registry/genboree_registry/by_canonicalid?canonicalid=CACN42032202"
        ]
      },
      "relation": "exactMatch"
    }
  ],
  "members": [
    {
      "id": "ga4gh:CX.Xb6kSRqlCY2VS1QJeKxhWyGqPfpPigf3",
      "type": "CopyNumberCount",
      "name": "NC_000023.11:g.(6978350_6996235)_(7564455_7594949)dup(2)",
      "description": "VRS variation of NC_000023.11:g.(6978350_6996235)_(7564455_7594949)dup, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
      "digest": "Xb6kSRqlCY2VS1QJeKxhWyGqPfpPigf3",
      "expressions": [
        {
          "syntax": "hgvs.g",
          "value": "NC_000023.11:g.(6978350_6996235)_(7564455_7594949)dup"
        }
      ],
      "location": {
        "id": "ga4gh:SL.XyercAFM_APQwFaDuPcXG5lHa4wUpkiL",
        "description": "Genomic region between positions 6,978,350-7,594,949 on chromosome X (refseq:NC_000023.11, GRCh38), with breakpoints estimated within the intervals 6,978,350-6,996,235 and 7,564,455-7,594,949.",
        "extensions": [
          {
            "name": "GRCh38 1-based, inclusive interval",
            "value": "chrX:(6978350\u20136996235)-(7564455\u20137594949)",
            "description": "Genomic region between positions 6,978,350-7,594,949 on chromosome X (refseq:NC_000023.11, GRCh38), with breakpoints estimated within the intervals 6,978,350-6,996,235 and 7,564,455-7,594,949; 1-based, inclusive interval notation."
          },
          {
            "name": "GRCh38 0-based, half-open interval",
            "value": "chrX:(6978349\u20136996235)-(7564454\u20137594949)",
            "description": "Genomic region between positions 6,978,349-7,594,949 on chromosome X (refseq:NC_000023.11, GRCh38), with breakpoints estimated within the intervals 6,978,349-6,996,235 and 7,564,454-7,594,949; 0-based, half-open interval notation."
          }
        ],
        "type": "SequenceLocation",
        "digest": "XyercAFM_APQwFaDuPcXG5lHa4wUpkiL",
        "sequenceReference": {
          "id": "refseq:NC_000023.11",
          "name": "NC_000023.11",
          "description": "Reference sequence for GRCh38 chromosome X.",
          "aliases": [
            "GRCh38:X",
            "GRCh38:chrX",
            "ga4gh:SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP"
          ],
          "type": "SequenceReference",
          "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul"
        },
        "start": [
          6978350,
          6996235
        ],
        "end": [
          7564455,
          7594949
        ]
      },
      "copies": 3
    }
  ]
}

Full example: YAML

id: clingen:cacn42032202
type: CategoricalVariant
name: GRCh38 Xp22.31(chrX:6978350-7594949)x3
description: An example categoricalCNV that uses CopyCountConstraint and uses ranges for start/end positions within the DefiningLocationConstraint.
aliases:
  - NC_000023.11:g.(6978350_6996235)_(7564455_7594949)dup(2)
  - GRCh37 (chrX:6896391_6914276-7482496_7512990)x3
  - NC_000023.10:g.(6896391_6914276-7482496_7512990)dup(2)
extensions:
  - name: cytogenetic location
    value: Xp22.31
constraints:
  - type: CopyCountConstraint
    copies: 3
  - type: DefiningLocationConstraint
    location:
      id: ga4gh:SL.XyercAFM_APQwFaDuPcXG5lHa4wUpkiL
      description: Genomic region between positions 6,978,350-7,594,949 on chromosome X (refseq:NC_000023.11, GRCh38), with breakpoints estimated within the intervals 6,978,350-6,996,235 and 7,564,455-7,594,949.
      extensions:
        - name: GRCh38 1-based, inclusive interval
          value: chrX:(6978350–6996235)-(7564455–7594949)
          description: Genomic region between positions 6,978,350-7,594,949 on chromosome X (refseq:NC_000023.11, GRCh38), with breakpoints estimated within the intervals 6,978,350-6,996,235 and 7,564,455-7,594,949; 1-based, inclusive interval notation.
        - name: GRCh38 0-based, half-open interval
          value: chrX:(6978349–6996235)-(7564454–7594949)
          description: Genomic region between positions 6,978,349-7,594,949 on chromosome X (refseq:NC_000023.11, GRCh38), with breakpoints estimated within the intervals 6,978,349-6,996,235 and 7,564,454-7,594,949; 0-based, half-open interval notation.
      type: SequenceLocation
      digest: XyercAFM_APQwFaDuPcXG5lHa4wUpkiL
      sequenceReference:
        id: refseq:NC_000023.11
        name: NC_000023.11
        description: Reference sequence for GRCh38 chromosome X.
        aliases:
          - GRCh38:X
          - GRCh38:chrX
          - ga4gh:SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP
        type: SequenceReference
        refgetAccession: SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul
      start:
        - 6978350
        - 6996235
      end:
        - 7564455
        - 7594949
    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://reg.clinicalgenome.org/
      code: CACN42032202
      iris:
        - https://reg.clinicalgenome.org/redmine/projects/Registry/genboree_registry/by_canonicalid?canonicalid=CACN42032202
    relation: exactMatch
members:
  - id: ga4gh:CX.Xb6kSRqlCY2VS1QJeKxhWyGqPfpPigf3
    type: CopyNumberCount
    name: NC_000023.11:g.(6978350_6996235)_(7564455_7594949)dup(2)
    description: VRS variation of NC_000023.11:g.(6978350_6996235)_(7564455_7594949)dup, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).
    digest: Xb6kSRqlCY2VS1QJeKxhWyGqPfpPigf3
    expressions:
      - syntax: hgvs.g
        value: NC_000023.11:g.(6978350_6996235)_(7564455_7594949)dup
    location:
      id: ga4gh:SL.XyercAFM_APQwFaDuPcXG5lHa4wUpkiL
      description: Genomic region between positions 6,978,350-7,594,949 on chromosome X (refseq:NC_000023.11, GRCh38), with breakpoints estimated within the intervals 6,978,350-6,996,235 and 7,564,455-7,594,949.
      extensions:
        - name: GRCh38 1-based, inclusive interval
          value: chrX:(6978350–6996235)-(7564455–7594949)
          description: Genomic region between positions 6,978,350-7,594,949 on chromosome X (refseq:NC_000023.11, GRCh38), with breakpoints estimated within the intervals 6,978,350-6,996,235 and 7,564,455-7,594,949; 1-based, inclusive interval notation.
        - name: GRCh38 0-based, half-open interval
          value: chrX:(6978349–6996235)-(7564454–7594949)
          description: Genomic region between positions 6,978,349-7,594,949 on chromosome X (refseq:NC_000023.11, GRCh38), with breakpoints estimated within the intervals 6,978,349-6,996,235 and 7,564,454-7,594,949; 0-based, half-open interval notation.
      type: SequenceLocation
      digest: XyercAFM_APQwFaDuPcXG5lHa4wUpkiL
      sequenceReference:
        id: refseq:NC_000023.11
        name: NC_000023.11
        description: Reference sequence for GRCh38 chromosome X.
        aliases:
          - GRCh38:X
          - GRCh38:chrX
          - ga4gh:SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP
        type: SequenceReference
        refgetAccession: SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul
      start:
        - 6978350
        - 6996235
      end:
        - 7564455
        - 7594949
    copies: 3