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NM_004958.4(MTOR):c.5992_5993del (p.Met1998fs)

Source

ClinVar variation 662001: NM_004958.4(MTOR):c.5992_5993del (p.Met1998fs)

Recipes that this example satisfies

Canonical Allele

Properties

id: clinvar:662001

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: NM_004958.4(MTOR):c.5992_5993del (p.Met1998fs)

The human-readable label listed within the Identifiers section of ClinVar’s Variant Details.

description: An example canonical allele.

This field was populated with an example value because ClinVar does not provide a longform description.

aliases: 7 HGVS expressions.

All listed HGVS representations within ClinVar’s Variant Details for the variant, including genomic, coding, protein, LRG, and RefSeqGene representations.

extensions: cytogenetic location, clinvar variation type, and hgvs list

The cytogenetic location (1p36.22) and ClinVar variation type (Deletion) are obtained from the Location and Type and length sections of ClinVar’s Variant Details. The hgvs list extension includes HGVS representations from ClinVar’s HGVS section, annotated with nucleotide type, MANE Select status, protein expression, and molecular consequence where applicable.

mappings: ClinVar, VarSome, and dbSNP

Mappings to ClinVar’s page for the variant, ClinGen, VarSome, and dbSNP are included from the Links section of ClinVar’s Variant Details.

Constraints

Defining Allele Constraint

The allele field is populated with the VRS Allele corresponding to the MANE Select coding representation NM_004958.4:c.5992_5993del, as included within members. The constraint includes relations specifying liftover and transcription relationships between the alleles.n.

Members

The members field includes two VRS Allele objects generated using the VICC Variation Normalizer from the hgvs.g and hgvs.c MANE Select representations of this variant: NC_000001.11:g.11128044_11128045del (GRCh38 genomic) and NM_004958.4:c.5992_5993del (MANE Select coding, on the MTOR MANE Select transcript refseq:NM_004958.4).

Full example: JSON

{
  "id": "clinvar:662001",
  "type": "CategoricalVariant",
  "name": "NM_004958.4(MTOR):c.5992_5993del (p.Met1998fs)",
  "description": "An example canonical allele.",
  "aliases": [
    "NM_004958.4:c.5992_5993del",
    "NC_000001.11:g.11128044_11128045del",
    "NC_000001.10:g.11188101_11188102del",
    "NP_004949.3:p.Met1998fs",
    "NG_033239.1:g.139507_139508del",
    "LRG_734:g.139507_139508del",
    "LRG_734t1:c.5992_5993del"
  ],
  "extensions": [
    {
      "name": "cytogenetic location",
      "value": "1p36.22"
    },
    {
      "name": "clinvar variation type",
      "value": "Deletion"
    },
    {
      "name": "hgvs list",
      "value": [
        {
          "nucleotideExpression": {
            "syntax": "hgvs.g",
            "value": "NC_000001.11:g.11128044_11128045del"
          },
          "nucleotideType": "genomic"
        },
        {
          "nucleotideExpression": {
            "syntax": "hgvs.c",
            "value": "NM_004958.4:c.5992_5993del"
          },
          "nucleotideType": "coding",
          "maneSelect": true,
          "proteinExpression": {
            "syntax": "hgvs.p",
            "value": "NP_004949.3:p.Met1998fs"
          },
          "molecularConsequence": {
            "name": "frameshift_variant",
            "system": "http://www.sequenceontology.org/browser/",
            "systemVersion": "release_2.5.3",
            "code": "SO:0001589",
            "iris": [
              "http://www.sequenceontology.org/browser/release_2.5.3/term/SO:0001589"
            ]
          }
        },
        {
          "nucleotideExpression": {
            "syntax": "hgvs.g",
            "value": "NG_033239.1:g.139507_139508del"
          },
          "nucleotideType": "genomic"
        },
        {
          "nucleotideExpression": {
            "syntax": "hgvs.g",
            "value": "LRG_734:g.139507_139508del"
          },
          "nucleotideType": "genomic"
        },
        {
          "nucleotideExpression": {
            "syntax": "hgvs.c",
            "value": "LRG_734t1:c.5992_5993del"
          },
          "nucleotideType": "coding"
        }
      ]
    }
  ],
  "constraints": [
    {
      "type": "DefiningAlleleConstraint",
      "allele": {
        "id": "ga4gh:VA.0TMQdMT2OBisJ9FI4tkzaBtxGB7r8FfJ",
        "type": "Allele",
        "name": "NM_004958.4:c.5992_5993del",
        "description": "VRS variation of NM_004958.4:c.5992_5993del, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
        "extensions": [
          {
            "name": "clinvar vcf",
            "value": "1-11128043-CAT-C"
          }
        ],
        "digest": "0TMQdMT2OBisJ9FI4tkzaBtxGB7r8FfJ",
        "expressions": [
          {
            "syntax": "spdi",
            "value": "NC_000001.11:11128043:AT:"
          },
          {
            "syntax": "hgvs.g",
            "value": "NC_000001.11:g.11128044_11128045del"
          },
          {
            "syntax": "hgvs.c",
            "value": "NM_004958.4:c.5992_5993del"
          },
          {
            "syntax": "hgvs.p",
            "value": "NP_004949.1:p.Met1998fs"
          }
        ],
        "location": {
          "id": "ga4gh:SL.gLe4d4Seuxn5fLCfO_2g34gF86vpGvo1",
          "description": "Coding DNA (cDNA) positions 5992 to 5993 of the MTOR MANE Select coding transcript (refseq:NM_004958.4), corresponding to genomic positions 11128044 to 11128045 on chromosome 1 (refseq:NC_000001.11, GRCh38).",
          "extensions": [
            {
              "name": "GRCh38 1-based, inclusive interval",
              "value": "chr1:11128044-11128045",
              "description": "Genomic positions 11128044 to 11128045 on chromosome 1 (refseq:NC_000001.11, GRCh38); 1-based, inclusive interval notation."
            },
            {
              "name": "GRCh38 0-based, half-open interval",
              "value": "chr1:11128043-11128045",
              "description": "Genomic positions 11128043 to 11128045 on chromosome 1 (refseq:NC_000001.11, GRCh38); 0-based, half-open interval notation."
            }
          ],
          "type": "SequenceLocation",
          "digest": "gLe4d4Seuxn5fLCfO_2g34gF86vpGvo1",
          "sequenceReference": {
            "id": "refseq:NM_004958.4",
            "name": "NM_004958.4",
            "description": "The MANE Select (GRCh38) coding transcript for MTOR.",
            "aliases": [
              "ensembl:ENST00000361445.9",
              "ga4gh:SQ.QheGYEnKbwNpM3LulbPTBQhyBSyZwuYm"
            ],
            "type": "SequenceReference",
            "refgetAccession": "SQ.QheGYEnKbwNpM3LulbPTBQhyBSyZwuYm",
            "residueAlphabet": "na"
          },
          "start": 6112,
          "end": 6114,
          "sequence": "AT"
        },
        "state": {
          "type": "ReferenceLengthExpression",
          "length": 0,
          "sequence": "",
          "repeatSubunitLength": 2
        }
      },
      "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://www.ncbi.nlm.nih.gov/clinvar",
        "code": "662001",
        "iris": [
          "https://www.ncbi.nlm.nih.gov/clinvar/variation/662001"
        ]
      },
      "relation": "exactMatch"
    },
    {
      "coding": {
        "system": "https://reg.clinicalgenome.org",
        "code": "CA915941124",
        "iris": [
          "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA915941124"
        ]
      },
      "relation": "relatedMatch"
    },
    {
      "coding": {
        "system": "https://varsome.com",
        "code": "hg38/rs1570942058",
        "iris": [
          "https://varsome.com/variant/hg38/rs1570942058"
        ]
      },
      "relation": "relatedMatch"
    },
    {
      "coding": {
        "system": "https://www.ncbi.nlm.nih.gov/snp",
        "code": "rs1570942058",
        "iris": [
          "https://www.ncbi.nlm.nih.gov/snp/rs1570942058"
        ]
      },
      "relation": "relatedMatch"
    }
  ],
  "members": [
    {
      "id": "ga4gh:VA.PN-6_l2_yI1UPBRCtFnWkR52iZXKVJ8b",
      "type": "Allele",
      "name": "NC_000001.11:g.11128044_11128045del",
      "description": "VRS variation of NC_000001.11:g.11128044_11128045del, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
      "extensions": [
        {
          "name": "clinvar_vcf",
          "value": "1-11128043-CAT-C"
        }
      ],
      "digest": "PN-6_l2_yI1UPBRCtFnWkR52iZXKVJ8b",
      "expressions": [
        {
          "syntax": "spdi",
          "value": "NC_000001.11:11128043:AT:"
        },
        {
          "syntax": "hgvs.g",
          "value": "NC_000001.11:g.11128044_11128045del"
        },
        {
          "syntax": "hgvs.c",
          "value": "NM_004958.4:c.5992_5993del"
        },
        {
          "syntax": "hgvs.p",
          "value": "NP_004949.1:p.Met1998fs"
        }
      ],
      "location": {
        "id": "ga4gh:SL.5-SKfXZ941W7JbZW3UmQKtijyUfd6d7z",
        "description": "Genomic positions 11,128,044 to 11,128,045 on chromosome 1 (refseq:NC_000001.11, GRCh38).",
        "extensions": [
          {
            "name": "GRCh38 1-based, inclusive interval",
            "value": "chr1:11128044-11128045",
            "description": "Genomic positions 11,128,044 to 11,128,045 on chromosome 1 (refseq:NC_000001.11, GRCh38); 1-based, inclusive interval notation."
          },
          {
            "name": "GRCh38 0-based, half-open interval",
            "value": "chr1:11128043-11128045",
            "description": "Genomic positions 11,128,043 to 11,128,045 on chromosome 1 (refseq:NC_000001.11, GRCh38); 0-based, half-open interval notation."
          }
        ],
        "type": "SequenceLocation",
        "digest": "5-SKfXZ941W7JbZW3UmQKtijyUfd6d7z",
        "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": 11128043,
        "end": 11128045,
        "sequence": "AT"
      },
      "state": {
        "type": "ReferenceLengthExpression",
        "length": 0,
        "sequence": "",
        "repeatSubunitLength": 2
      }
    },
    {
      "id": "ga4gh:VA.0TMQdMT2OBisJ9FI4tkzaBtxGB7r8FfJ",
      "type": "Allele",
      "name": "NM_004958.4:c.5992_5993del",
      "description": "VRS variation of NM_004958.4:c.5992_5993del, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
      "extensions": [
        {
          "name": "clinvar vcf",
          "value": "1-11128043-CAT-C"
        }
      ],
      "digest": "0TMQdMT2OBisJ9FI4tkzaBtxGB7r8FfJ",
      "expressions": [
        {
          "syntax": "spdi",
          "value": "NC_000001.11:11128043:AT:"
        },
        {
          "syntax": "hgvs.g",
          "value": "NC_000001.11:g.11128044_11128045del"
        },
        {
          "syntax": "hgvs.c",
          "value": "NM_004958.4:c.5992_5993del"
        },
        {
          "syntax": "hgvs.p",
          "value": "NP_004949.1:p.Met1998fs"
        }
      ],
      "location": {
        "id": "ga4gh:SL.gLe4d4Seuxn5fLCfO_2g34gF86vpGvo1",
        "description": "Coding DNA (cDNA) positions 5992 to 5993 of the MTOR MANE Select coding transcript (refseq:NM_004958.4), corresponding to genomic positions 11128044 to 11128045 on chromosome 1 (refseq:NC_000001.11, GRCh38).",
        "extensions": [
          {
            "name": "GRCh38 1-based, inclusive interval",
            "value": "chr1:11128044-11128045",
            "description": "Genomic positions 11128044 to 11128045 on chromosome 1 (refseq:NC_000001.11, GRCh38); 1-based, inclusive interval notation."
          },
          {
            "name": "GRCh38 0-based, half-open interval",
            "value": "chr1:11128043-11128045",
            "description": "Genomic positions 11128043 to 11128045 on chromosome 1 (refseq:NC_000001.11, GRCh38); 0-based, half-open interval notation."
          }
        ],
        "type": "SequenceLocation",
        "digest": "gLe4d4Seuxn5fLCfO_2g34gF86vpGvo1",
        "sequenceReference": {
          "id": "refseq:NM_004958.4",
          "name": "NM_004958.4",
          "description": "The MANE Select (GRCh38) coding transcript for MTOR.",
          "aliases": [
            "ensembl:ENST00000361445.9",
            "ga4gh:SQ.QheGYEnKbwNpM3LulbPTBQhyBSyZwuYm"
          ],
          "type": "SequenceReference",
          "refgetAccession": "SQ.QheGYEnKbwNpM3LulbPTBQhyBSyZwuYm",
          "residueAlphabet": "na"
        },
        "start": 6112,
        "end": 6114,
        "sequence": "AT"
      },
      "state": {
        "type": "ReferenceLengthExpression",
        "length": 0,
        "sequence": "",
        "repeatSubunitLength": 2
      }
    }
  ]
}

Full example: YAML

id: clinvar:662001
type: CategoricalVariant
name: NM_004958.4(MTOR):c.5992_5993del (p.Met1998fs)
description: An example canonical allele.
aliases:
  - NM_004958.4:c.5992_5993del
  - NC_000001.11:g.11128044_11128045del
  - NC_000001.10:g.11188101_11188102del
  - NP_004949.3:p.Met1998fs
  - NG_033239.1:g.139507_139508del
  - LRG_734:g.139507_139508del
  - LRG_734t1:c.5992_5993del
extensions:
  - name: cytogenetic location
    value: 1p36.22
  - name: clinvar variation type
    value: Deletion
  - name: hgvs list
    value:
      - nucleotideExpression:
          syntax: hgvs.g
          value: NC_000001.11:g.11128044_11128045del
        nucleotideType: genomic
      - nucleotideExpression:
          syntax: hgvs.c
          value: NM_004958.4:c.5992_5993del
        nucleotideType: coding
        maneSelect: true
        proteinExpression:
          syntax: hgvs.p
          value: NP_004949.3:p.Met1998fs
        molecularConsequence:
          name: frameshift_variant
          system: http://www.sequenceontology.org/browser/
          systemVersion: release_2.5.3
          code: SO:0001589
          iris:
            - http://www.sequenceontology.org/browser/release_2.5.3/term/SO:0001589
      - nucleotideExpression:
          syntax: hgvs.g
          value: NG_033239.1:g.139507_139508del
        nucleotideType: genomic
      - nucleotideExpression:
          syntax: hgvs.g
          value: LRG_734:g.139507_139508del
        nucleotideType: genomic
      - nucleotideExpression:
          syntax: hgvs.c
          value: LRG_734t1:c.5992_5993del
        nucleotideType: coding
constraints:
  - type: DefiningAlleleConstraint
    allele:
      id: ga4gh:VA.0TMQdMT2OBisJ9FI4tkzaBtxGB7r8FfJ
      type: Allele
      name: NM_004958.4:c.5992_5993del
      description: VRS variation of NM_004958.4:c.5992_5993del, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).
      extensions:
        - name: clinvar vcf
          value: 1-11128043-CAT-C
      digest: 0TMQdMT2OBisJ9FI4tkzaBtxGB7r8FfJ
      expressions:
        - syntax: spdi
          value: 'NC_000001.11:11128043:AT:'
        - syntax: hgvs.g
          value: NC_000001.11:g.11128044_11128045del
        - syntax: hgvs.c
          value: NM_004958.4:c.5992_5993del
        - syntax: hgvs.p
          value: NP_004949.1:p.Met1998fs
      location:
        id: ga4gh:SL.gLe4d4Seuxn5fLCfO_2g34gF86vpGvo1
        description: Coding DNA (cDNA) positions 5992 to 5993 of the MTOR MANE Select coding transcript (refseq:NM_004958.4), corresponding to genomic positions 11128044 to 11128045 on chromosome 1 (refseq:NC_000001.11, GRCh38).
        extensions:
          - name: GRCh38 1-based, inclusive interval
            value: chr1:11128044-11128045
            description: Genomic positions 11128044 to 11128045 on chromosome 1 (refseq:NC_000001.11, GRCh38); 1-based, inclusive interval notation.
          - name: GRCh38 0-based, half-open interval
            value: chr1:11128043-11128045
            description: Genomic positions 11128043 to 11128045 on chromosome 1 (refseq:NC_000001.11, GRCh38); 0-based, half-open interval notation.
        type: SequenceLocation
        digest: gLe4d4Seuxn5fLCfO_2g34gF86vpGvo1
        sequenceReference:
          id: refseq:NM_004958.4
          name: NM_004958.4
          description: The MANE Select (GRCh38) coding transcript for MTOR.
          aliases:
            - ensembl:ENST00000361445.9
            - ga4gh:SQ.QheGYEnKbwNpM3LulbPTBQhyBSyZwuYm
          type: SequenceReference
          refgetAccession: SQ.QheGYEnKbwNpM3LulbPTBQhyBSyZwuYm
          residueAlphabet: na
        start: 6112
        end: 6114
        sequence: AT
      state:
        type: ReferenceLengthExpression
        length: 0
        sequence: ''
        repeatSubunitLength: 2
    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://www.ncbi.nlm.nih.gov/clinvar
      code: '662001'
      iris:
        - https://www.ncbi.nlm.nih.gov/clinvar/variation/662001
    relation: exactMatch
  - coding:
      system: https://reg.clinicalgenome.org
      code: CA915941124
      iris:
        - https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA915941124
    relation: relatedMatch
  - coding:
      system: https://varsome.com
      code: hg38/rs1570942058
      iris:
        - https://varsome.com/variant/hg38/rs1570942058
    relation: relatedMatch
  - coding:
      system: https://www.ncbi.nlm.nih.gov/snp
      code: rs1570942058
      iris:
        - https://www.ncbi.nlm.nih.gov/snp/rs1570942058
    relation: relatedMatch
members:
  - id: ga4gh:VA.PN-6_l2_yI1UPBRCtFnWkR52iZXKVJ8b
    type: Allele
    name: NC_000001.11:g.11128044_11128045del
    description: VRS variation of NC_000001.11:g.11128044_11128045del, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).
    extensions:
      - name: clinvar_vcf
        value: 1-11128043-CAT-C
    digest: PN-6_l2_yI1UPBRCtFnWkR52iZXKVJ8b
    expressions:
      - syntax: spdi
        value: 'NC_000001.11:11128043:AT:'
      - syntax: hgvs.g
        value: NC_000001.11:g.11128044_11128045del
      - syntax: hgvs.c
        value: NM_004958.4:c.5992_5993del
      - syntax: hgvs.p
        value: NP_004949.1:p.Met1998fs
    location:
      id: ga4gh:SL.5-SKfXZ941W7JbZW3UmQKtijyUfd6d7z
      description: Genomic positions 11,128,044 to 11,128,045 on chromosome 1 (refseq:NC_000001.11, GRCh38).
      extensions:
        - name: GRCh38 1-based, inclusive interval
          value: chr1:11128044-11128045
          description: Genomic positions 11,128,044 to 11,128,045 on chromosome 1 (refseq:NC_000001.11, GRCh38); 1-based, inclusive interval notation.
        - name: GRCh38 0-based, half-open interval
          value: chr1:11128043-11128045
          description: Genomic positions 11,128,043 to 11,128,045 on chromosome 1 (refseq:NC_000001.11, GRCh38); 0-based, half-open interval notation.
      type: SequenceLocation
      digest: 5-SKfXZ941W7JbZW3UmQKtijyUfd6d7z
      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: 11128043
      end: 11128045
      sequence: AT
    state:
      type: ReferenceLengthExpression
      length: 0
      sequence: ''
      repeatSubunitLength: 2
  - id: ga4gh:VA.0TMQdMT2OBisJ9FI4tkzaBtxGB7r8FfJ
    type: Allele
    name: NM_004958.4:c.5992_5993del
    description: VRS variation of NM_004958.4:c.5992_5993del, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).
    extensions:
      - name: clinvar vcf
        value: 1-11128043-CAT-C
    digest: 0TMQdMT2OBisJ9FI4tkzaBtxGB7r8FfJ
    expressions:
      - syntax: spdi
        value: 'NC_000001.11:11128043:AT:'
      - syntax: hgvs.g
        value: NC_000001.11:g.11128044_11128045del
      - syntax: hgvs.c
        value: NM_004958.4:c.5992_5993del
      - syntax: hgvs.p
        value: NP_004949.1:p.Met1998fs
    location:
      id: ga4gh:SL.gLe4d4Seuxn5fLCfO_2g34gF86vpGvo1
      description: Coding DNA (cDNA) positions 5992 to 5993 of the MTOR MANE Select coding transcript (refseq:NM_004958.4), corresponding to genomic positions 11128044 to 11128045 on chromosome 1 (refseq:NC_000001.11, GRCh38).
      extensions:
        - name: GRCh38 1-based, inclusive interval
          value: chr1:11128044-11128045
          description: Genomic positions 11128044 to 11128045 on chromosome 1 (refseq:NC_000001.11, GRCh38); 1-based, inclusive interval notation.
        - name: GRCh38 0-based, half-open interval
          value: chr1:11128043-11128045
          description: Genomic positions 11128043 to 11128045 on chromosome 1 (refseq:NC_000001.11, GRCh38); 0-based, half-open interval notation.
      type: SequenceLocation
      digest: gLe4d4Seuxn5fLCfO_2g34gF86vpGvo1
      sequenceReference:
        id: refseq:NM_004958.4
        name: NM_004958.4
        description: The MANE Select (GRCh38) coding transcript for MTOR.
        aliases:
            - ensembl:ENST00000361445.9
            - ga4gh:SQ.QheGYEnKbwNpM3LulbPTBQhyBSyZwuYm
        type: SequenceReference
        refgetAccession: SQ.QheGYEnKbwNpM3LulbPTBQhyBSyZwuYm
        residueAlphabet: na
      start: 6112
      end: 6114
      sequence: AT
    state:
      type: ReferenceLengthExpression
      length: 0
      sequence: ''
      repeatSubunitLength: 2