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
Attributes
id: clinvar:662001, where 662001 is the Variation ID listed within the Identifiers section of ClinVar’s Variant Details.type: CategoricalVariant, as required by the specification.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: A brief placeholder note, as ClinVar does not contain a longform description of this variant.aliases: All listed HGVS representations within ClinVar’s Variant Details for the variant, including genomic, coding, protein, LRG, and RefSeqGene representations.extensions: 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: 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.
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