Defining Allele Constraint
Definition and Information Model
Note
This data class is at a trial use maturity level and may change in future releases. Maturity levels are described in the GKS Maturity Model.
Computational Definition
The defining allele and its associated relationships that are congruent with member variants.
Information Model
Some DefiningAlleleConstraint attributes are inherited from Constraint.
Field |
Flags |
Type |
Limits |
Description |
|---|---|---|---|---|
type |
string |
1..1 |
MUST be “DefiningAlleleConstraint” |
|
allele |
1..1 |
|||
relations |
⋮ | 0..m |
Defined relationships from which members relate to the defining allele. |
Examples
The following are example implementations of DefiningAlleleConstraint:
NM_004958.4(MTOR):c.5992_5993del (p.Met1998fs)
{
"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"
]
}
}
]
}
NC_000001.11:g.1699974C>G
{
"type": "DefiningAlleleConstraint",
"allele": {
"id": "ga4gh:VA.WjRY1EXgci6Nd0M2yI86Ue_OOnfnb-Ss",
"type": "Allele",
"name": "NC_000001.11:g.1699974C>G",
"description": "VRS Allele of NC_000001.11:g.1699974C>G, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "WjRY1EXgci6Nd0M2yI86Ue_OOnfnb-Ss",
"expressions": [
{
"syntax": "hgvs.g",
"value": "NC_000001.11:g.1699974C>G"
}
],
"location": {
"id": "ga4gh:SL.YmbtK6FLqlk2bLjpFwH-y7k4RLq_t7L3",
"description": "Genomic position 1699974 on chromosome 1 (refseq:NC_000001.11, GRCh38).",
"extensions": [
{
"name": "GRCh38 1-based, genomic position",
"value": "chr1:1699974",
"description": "Genomic position 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38)."
},
{
"name": "GRCh38 1-based, inclusive interval notation",
"value": "chr1:1699974-1699974",
"description": "Genomic positions 1,699,974 to 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval notation",
"value": "chr1:1699973-1699974",
"description": "Genomic positions 1,699,973 to 1,699,974 on chromosome 1 (refseq:NC_000001.11, GRCh38); 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "YmbtK6FLqlk2bLjpFwH-y7k4RLq_t7L3",
"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": 1699973,
"end": 1699974,
"sequence": "C"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "G"
}
},
"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"
]
}
}
]
}
EGFR L858R
{
"type": "DefiningAlleleConstraint",
"allele": {
"id": "ga4gh:VA.S41CcMJT2bcd8R4-qXZWH1PoHWNtG2PZ",
"type": "Allele",
"name": "NP_005219.2:p.Leu858Arg",
"description": "VRS variation of NP_005219.2:p.Leu858Arg, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "S41CcMJT2bcd8R4-qXZWH1PoHWNtG2PZ",
"expressions": [
{
"syntax": "hgvs.p",
"value": "NP_005219.2:p.Leu858Arg"
}
],
"location": {
"id": "ga4gh:SL.v0_edynH98OIu-0QPVT5anCSOriAFSDQ",
"description": "Amino acid position 858 within the EGFR protein (refseq:NP_005219.2), which is the protein product of the MANE Select (GRCh38) coding transcript for EGFR (refseq:NM_005228.5), corresponding to leucine in the reference sequence.",
"type": "SequenceLocation",
"digest": "v0_edynH98OIu-0QPVT5anCSOriAFSDQ",
"sequenceReference": {
"id": "refseq:NP_005219.2",
"name": "NP_005219.2",
"description": "The protein product of the MANE Select (GRCh38) coding transcript for EGFR (refseq:NM_005228.5), corresponding to the RefSeq protein accession NP_005219.2.",
"aliases": [
"ensembl:ENSP00000275493.2",
"ga4gh:SQ.vyo55F6mA6n2LgN4cagcdRzOuh38V4mE"
],
"type": "SequenceReference",
"refgetAccession": "SQ.vyo55F6mA6n2LgN4cagcdRzOuh38V4mE",
"residueAlphabet": "aa"
},
"start": 857,
"end": 858,
"sequence": "L"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "R"
}
},
"relations": [
{
"primaryCoding": {
"code": "translation_of",
"system": "http://www.sequenceontology.org",
"iris": [
"http://www.sequenceontology.org/browser/current_release/term/translation_of"
]
}
}
]
}
NM_007294.4(BRCA1):c.5558dup (p.Tyr1853Ter)
{
"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"
]
}
}
]
}