EGFR L858R
Source
CIViC variant id 33: EGFR L858R
Recipes that this example satisfies
Properties
id: civic.mpid:33CIViC Molecular Profile ID, where mpid stands for Molecular Profile ID, derived from the Molecular Profile ID contained within the CIViC URL for this genomic alteration.
type: CategoricalVariantThis value is required by the specification for all Categorical Variant objects.
name: EGFR L858RHuman-readable label given to the genomic alteration by CIViC.
description: The longform description of EGFR L858R as provided by CIViC.This mutation is one of the most prevalent single mutations in lung cancer and confers sensitivity to TKI therapies.
aliases: LEU858ARG, rs121434568, and HGVS expressionsAll aliases, HGVS descriptions, and the MANE Select transcript listed for EGFR L858R within the Summary section of CIViC’s variant page, including genomic and coding HGVS representations, and the protein representation NP_005219.2:p.Leu858Arg.
extensions: CIViC Representative Variant Coordinates, CIViC Variant Type, hgvs list, and CIViC Molecular Profile ScoreThe CIViC Representative Variant Coordinates and CIViC Variant Type (missense_variant, SO:0001583) are sourced from the Representative Variant Coordinates and Variant Type sections of CIViC’s Variant Summary. The hgvs list extension contains the HGVS descriptions and MANE Select transcript representations from CIViC. A CIViC Molecular Profile Score extension is also included.
mappings: CIViC, ClinGen, ClinVar, and dbSNPMappings to CIViC’s variant and molecular profile pages, ClinGen, ClinVar entries for multiple nucleotide change representations, and dbSNP are included.
Constraints
- Defining Allele Constraint
The
allelefield is populated with the VRS Allele corresponding to the hgvs.p representation NP_005219.2:p.Leu858Arg, as included withinmembers. The constraint includes a translation_of relation to link the protein allele to the coding DNA representation.
Members
The members field includes three VRS Allele objects generated using the VICC Variation Normalizer:
NC_000007.13:g.55259515T>G (hgvs.g, GRCh37)
NM_005228.5:c.2573T>G (hgvs.c, on the MANE Select transcript for EGFR refseq:NM_005228.5)
NP_005219.2:p.Leu858Arg (hgvs.p, on the protein product of the MANE Select transcript refseq:NP_005219.2)
Full example: JSON
{
"id": "civic.mpid:33",
"type": "CategoricalVariant",
"name": "EGFR L858R",
"description": "EGFR L858R has long been recognized as a functionally significant mutation in cancer, and is one of the most prevalent single mutations in lung cancer. Best described in non-small cell lung cancer (NSCLC), the mutation seems to confer sensitivity to first and second generation TKI's like gefitinib and neratinib. NSCLC patients with this mutation treated with TKI's show increased overall and progression-free survival, as compared to chemotherapy alone. Third generation TKI's are currently in clinical trials that specifically focus on mutant forms of EGFR, a few of which have shown efficacy in treating patients that failed to respond to earlier generation TKI therapies.",
"aliases": [
"LEU858ARG",
"rs121434568",
"L813R",
"LEU813ARG",
"NC_000007.13:g.55259515T>G",
"NM_005228.4:c.2573T>G",
"ENST00000275493.2:c.2573T>G",
"ENST00000275493.7:c.2573T>G",
"NP_005219.2:p.Leu858Arg"
],
"extensions": [
{
"name": "CIViC Representative Variant Coordinates",
"value": {
"chromosome": "7",
"start": 55259515,
"stop": 55259515,
"reference_bases": "T",
"variant_bases": "G",
"representative_transcript": "ENST00000275493.2",
"ensembl_version": 75,
"reference_build": "GRCh37"
}
},
{
"name": "CIViC Variant Type",
"value": {
"name": "missense_variant",
"system": "http://www.sequenceontology.org/browser/",
"systemVersion": "release_2.5.3",
"code": "SO:0001583",
"iris": [
"http://www.sequenceontology.org/browser/release_2.5.3/term/SO:0001583"
]
}
},
{
"name": "CIViC Molecular Profile Score",
"value": 379
},
{
"name": "hgvs list",
"value": [
{
"nucleotideExpression": {
"syntax": "hgvs.g",
"value": "NC_000007.13:g.55259515T>G"
},
"nucleotideType": "genomic"
},
{
"nucleotideExpression": {
"syntax": "hgvs.c",
"value": "NM_005228.5:c.2573T>G"
},
"nucleotideType": "coding"
},
{
"nucleotideExpression": {
"syntax": "hgvs.c",
"value": "ENST00000275493.2:c.2573T>G"
},
"nucleotideType": "coding"
},
{
"nucleotideExpression": {
"syntax": "hgvs.c",
"value": "ENST00000275493.7:c.2573T>G"
},
"nucleotideType": "coding",
"maneSelect": true,
"proteinExpression": {
"syntax": "hgvs.p",
"value": "NP_005219.2:p.Leu858Arg"
},
"molecularConsequence": {
"name": "missense_variant",
"system": "http://www.sequenceontology.org/browser/",
"systemVersion": "release_2.5.3",
"code": "SO:0001583",
"iris": [
"http://www.sequenceontology.org/browser/release_2.5.3/term/SO:0001583"
]
}
}
]
}
],
"constraints": [
{
"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"
]
}
}
]
}
],
"mappings": [
{
"coding": {
"system": "https://civicdb.org/variants/",
"code": "33",
"iris": [
"https://civicdb.org/variants/33/summary"
]
},
"relation": "exactMatch"
},
{
"coding": {
"system": "https://civicdb.org/molecular-profiles/",
"code": "33",
"iris": [
"https://civicdb.org/molecular-profiles/33/summary"
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://reg.clinicalgenome.org/",
"code": "CA126713",
"iris": [
"https://reg.genome.network/redmine/projects/registry/genboree_registry/by_caid?caid=CA126713"
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/clinvar/variation/",
"code": "16609",
"iris": [
"https://www.ncbi.nlm.nih.gov/clinvar/variation/16609/"
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/clinvar/variation/",
"code": "376282",
"iris": [
"https://www.ncbi.nlm.nih.gov/clinvar/variation/376282/"
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/clinvar/variation/",
"code": "376280",
"iris": [
"https://www.ncbi.nlm.nih.gov/clinvar/variation/376280/"
]
},
"relation": "relatedMatch"
},
{
"coding": {
"system": "https://www.ncbi.nlm.nih.gov/snp/",
"code": "rs121434568",
"iris": [
"https://www.ncbi.nlm.nih.gov/snp/rs121434568"
]
},
"relation": "relatedMatch"
}
],
"members": [
{
"id": "ga4gh:VA.7WF8GDGgqy8ksDf9KV-qrWS_2_q8fiEO",
"type": "Allele",
"name": "NC_000007.13:g.55259515T>G",
"description": "VRS variation of NC_000007.13:g.55259515T>G, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "7WF8GDGgqy8ksDf9KV-qrWS_2_q8fiEO",
"expressions": [
{
"syntax": "hgvs.g",
"value": "NC_000007.13:g.55259515T>G"
},
{
"syntax": "hgvs.c",
"value": "NM_005228.5:c.2573T>G"
},
{
"syntax": "hgvs.p",
"value": "NP_005219.2:p.Leu858Arg"
}
],
"location": {
"id": "ga4gh:SL.FYIfdQ3NyatgqPT_kKMfeIbt00559Izo",
"description": "Genomic position 55,259,515 on chromosome 1 (refseq:NC_000007.13, GRCh38).",
"extensions": [
{
"name": "GRCh38 1-based, genomic position",
"value": "chr7:55259515",
"description": "Genomic position 55,259,515 on chromosome 1 (refseq:NC_000007.13, GRCh38)."
},
{
"name": "GRCh38 1-based, inclusive interval notation",
"value": "chr1:55259515-55259515",
"description": "Genomic positions 55,259,515 to 55,259,515 on chromosome 1 (refseq:NC_000007.13, GRCh38); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval notation",
"value": "chr1:55259514-55259515",
"description": "Genomic positions 55,259,514 to 55,259,515 on chromosome 1 (refseq:NC_000007.13, GRCh38); 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "FYIfdQ3NyatgqPT_kKMfeIbt00559Izo",
"sequenceReference": {
"id": "refseq:NC_000007.13",
"name": "NC_000007.13",
"description": "Reference sequence for GRCh38 chromosome 7.",
"aliases": [
"GRCh38:7",
"GRCh38:chr7",
"ga4gh:SQ.IW78mgV5Cqf6M24hy52hPjyyo5tCCd86"
],
"type": "SequenceReference",
"refgetAccession": "SQ.IW78mgV5Cqf6M24hy52hPjyyo5tCCd86",
"residueAlphabet": "na"
},
"start": 55259514,
"end": 55259515,
"sequence": "AT"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "G"
}
},
{
"id": "ga4gh:VA.gV7_dnvF8SQSeUdvgDFhU65zK_csc6VE",
"type": "Allele",
"name": "NM_005228.5:c.2573T>G",
"description": "VRS variation of NM_005228.5:c.2573T>G, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
"digest": "gV7_dnvF8SQSeUdvgDFhU65zK_csc6VE",
"expressions": [
{
"syntax": "hgvs.g",
"value": "NC_000007.13:g.55259515T>G"
},
{
"syntax": "hgvs.c",
"value": "NM_005228.5:c.2573T>G"
},
{
"syntax": "hgvs.p",
"value": "NP_005219.2:p.Leu858Arg"
}
],
"location": {
"id": "ga4gh:SL.LREsUiEYvOrRhwXW1rG72kXFPegvkNzI",
"description": "Coding DNA (cDNA) position 2573 of the EGFR MANE Select coding transcript (refseq:NM_005228.5), corresponding to genomic position 55259515 on chromosome 7 (refseq:NC_000007.13, GRCh38).",
"extensions": [
{
"name": "GRCh38 1-based, genomic position",
"value": "chr7:55259515",
"description": "Genomic position 55,259,515 on chromosome 1 (refseq:NC_000007.13, GRCh38)."
},
{
"name": "GRCh38 1-based, inclusive interval notation",
"value": "chr7:55259515-55259515",
"description": "Genomic positions 55,259,515 to 55,259,515 on chromosome 1 (refseq:NC_000007.13, GRCh38); 1-based, inclusive interval notation."
},
{
"name": "GRCh38 0-based, half-open interval notation",
"value": "chr7:55259514-55259515",
"description": "Genomic positions 55,259,514 to 55,259,515 on chromosome 1 (refseq:NC_000007.13, GRCh38); 0-based, half-open interval notation."
}
],
"type": "SequenceLocation",
"digest": "LREsUiEYvOrRhwXW1rG72kXFPegvkNzI",
"sequenceReference": {
"id": "refseq:NM_005228.5",
"name": "NM_005228.5",
"description": "The MANE Select (GRCh38) coding transcript for EGFR.",
"aliases": [
"ensembl:ENST00000275493.7",
"ga4gh:SQ.d_QsP29RWJi6bac7GOC9cJ9AO7s_HUMN"
],
"type": "SequenceReference",
"refgetAccession": "SQ.d_QsP29RWJi6bac7GOC9cJ9AO7s_HUMN",
"residueAlphabet": "na"
},
"start": 2833,
"end": 2834,
"sequence": "T"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "G"
}
},
{
"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.g",
"value": "NC_000007.13:g.55259515T>G"
},
{
"syntax": "hgvs.c",
"value": "NM_005228.5:c.2573T>G"
},
{
"syntax": "hgvs.p",
"value": "NP_005219.2:p.Leu858Arg"
}
],
"location": {
"id": "ga4gh:SL.v0_edynH98OIu-0QPVT5anCSOriAFSDQ",
"description": "Amino acid position 858 of the RefSeq protein NP_005219.2, which is the protein product of the MANE Select (GRCh38) coding transcript for EGFR (refseq:NM_005228.5).",
"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"
}
}
]
}
Full example: YAML
id: civic.mpid:33
type: CategoricalVariant
name: EGFR L858R
description: >-
EGFR L858R has long been recognized as a functionally significant mutation in cancer,
and is one of the most prevalent single mutations in lung cancer. Best described in
non-small cell lung cancer (NSCLC), the mutation seems to confer sensitivity to first
and second generation TKI's like gefitinib and neratinib. NSCLC patients with this
mutation treated with TKI's show increased overall and progression-free survival, as
compared to chemotherapy alone. Third generation TKI's are currently in clinical trials
that specifically focus on mutant forms of EGFR, a few of which have shown efficacy in
treating patients that failed to respond to earlier generation TKI therapies.
aliases:
- LEU858ARG
- rs121434568
- L813R
- LEU813ARG
- NC_000007.13:g.55259515T>G
- NM_005228.4:c.2573T>G
- ENST00000275493.2:c.2573T>G
- ENST00000275493.7:c.2573T>G
- NP_005219.2:p.Leu858Arg
extensions:
- name: CIViC Representative Variant Coordinates
value:
chromosome: '7'
start: 55259515
stop: 55259515
reference_bases: T
variant_bases: G
representative_transcript: ENST00000275493.2
ensembl_version: 75
reference_build: GRCh37
- name: CIViC Variant Type
value:
name: missense_variant
system: http://www.sequenceontology.org/browser/
systemVersion: release_2.5.3
code: SO:0001583
iris:
- http://www.sequenceontology.org/browser/release_2.5.3/term/SO:0001583
- name: CIViC Molecular Profile Score
value: 379
- name: hgvs list
value:
- nucleotideExpression:
syntax: hgvs.g
value: NC_000007.13:g.55259515T>G
nucleotideType: genomic
- nucleotideExpression:
syntax: hgvs.c
value: NM_005228.5:c.2573T>G
nucleotideType: coding
- nucleotideExpression:
syntax: hgvs.c
value: ENST00000275493.2:c.2573T>G
nucleotideType: coding
- nucleotideExpression:
syntax: hgvs.c
value: ENST00000275493.7:c.2573T>G
nucleotideType: coding
maneSelect: true
proteinExpression:
syntax: hgvs.p
value: NP_005219.2:p.Leu858Arg
molecularConsequence:
name: missense_variant
system: http://www.sequenceontology.org/browser/
systemVersion: release_2.5.3
code: SO:0001583
iris:
- http://www.sequenceontology.org/browser/release_2.5.3/term/SO:0001583
constraints:
- 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
mappings:
- coding:
system: https://civicdb.org/variants/
code: '33'
iris:
- https://civicdb.org/variants/33/summary
relation: exactMatch
- coding:
system: https://civicdb.org/molecular-profiles/
code: '33'
iris:
- https://civicdb.org/molecular-profiles/33/summary
relation: relatedMatch
- coding:
system: https://reg.clinicalgenome.org/
code: CA126713
iris:
- https://reg.genome.network/redmine/projects/registry/genboree_registry/by_caid?caid=CA126713
relation: relatedMatch
- coding:
system: https://www.ncbi.nlm.nih.gov/clinvar/variation/
code: '16609'
iris:
- https://www.ncbi.nlm.nih.gov/clinvar/variation/16609/
relation: relatedMatch
- coding:
system: https://www.ncbi.nlm.nih.gov/clinvar/variation/
code: '376282'
iris:
- https://www.ncbi.nlm.nih.gov/clinvar/variation/376282/
relation: relatedMatch
- coding:
system: https://www.ncbi.nlm.nih.gov/clinvar/variation/
code: '376280'
iris:
- https://www.ncbi.nlm.nih.gov/clinvar/variation/376280/
relation: relatedMatch
- coding:
system: https://www.ncbi.nlm.nih.gov/snp/
code: rs121434568
iris:
- https://www.ncbi.nlm.nih.gov/snp/rs121434568
relation: relatedMatch
members:
- id: ga4gh:VA.7WF8GDGgqy8ksDf9KV-qrWS_2_q8fiEO
type: Allele
name: NC_000007.13:g.55259515T>G
description: VRS variation of NC_000007.13:g.55259515T>G, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).
digest: 7WF8GDGgqy8ksDf9KV-qrWS_2_q8fiEO
expressions:
- syntax: hgvs.g
value: NC_000007.13:g.55259515T>G
- syntax: hgvs.c
value: NM_005228.5:c.2573T>G
- syntax: hgvs.p
value: NP_005219.2:p.Leu858Arg
location:
id: ga4gh:SL.FYIfdQ3NyatgqPT_kKMfeIbt00559Izo
description: Genomic position 55,259,515 on chromosome 1 (refseq:NC_000007.13, GRCh38).
extensions:
- name: GRCh38 1-based, genomic position
value: chr7:55259515
description: Genomic position 55,259,515 on chromosome 1 (refseq:NC_000007.13, GRCh38).
- name: GRCh38 1-based, inclusive interval notation
value: chr1:55259515-55259515
description: Genomic positions 55,259,515 to 55,259,515 on chromosome 1 (refseq:NC_000007.13, GRCh38); 1-based, inclusive interval notation.
- name: GRCh38 0-based, half-open interval notation
value: chr1:55259514-55259515
description: Genomic positions 55,259,514 to 55,259,515 on chromosome 1 (refseq:NC_000007.13, GRCh38); 0-based, half-open interval notation.
type: SequenceLocation
digest: FYIfdQ3NyatgqPT_kKMfeIbt00559Izo
sequenceReference:
id: refseq:NC_000007.13
name: NC_000007.13
description: Reference sequence for GRCh38 chromosome 7.
aliases:
- GRCh38:7
- GRCh38:chr7
- ga4gh:SQ.IW78mgV5Cqf6M24hy52hPjyyo5tCCd86
type: SequenceReference
refgetAccession: SQ.IW78mgV5Cqf6M24hy52hPjyyo5tCCd86
residueAlphabet: na
start: 55259514
end: 55259515
sequence: AT
state:
type: LiteralSequenceExpression
sequence: G
- id: ga4gh:VA.gV7_dnvF8SQSeUdvgDFhU65zK_csc6VE
type: Allele
name: NM_005228.5:c.2573T>G
description: VRS variation of NM_005228.5:c.2573T>G, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).
digest: gV7_dnvF8SQSeUdvgDFhU65zK_csc6VE
expressions:
- syntax: hgvs.g
value: NC_000007.13:g.55259515T>G
- syntax: hgvs.c
value: NM_005228.5:c.2573T>G
- syntax: hgvs.p
value: NP_005219.2:p.Leu858Arg
location:
id: ga4gh:SL.LREsUiEYvOrRhwXW1rG72kXFPegvkNzI
description: Coding DNA (cDNA) position 2573 of the EGFR MANE Select coding transcript (refseq:NM_005228.5), corresponding to genomic position 55259515 on chromosome 7 (refseq:NC_000007.13, GRCh38).
extensions:
- name: GRCh38 1-based, genomic position
value: chr7:55259515
description: Genomic position 55,259,515 on chromosome 1 (refseq:NC_000007.13, GRCh38).
- name: GRCh38 1-based, inclusive interval notation
value: chr7:55259515-55259515
description: Genomic positions 55,259,515 to 55,259,515 on chromosome 1 (refseq:NC_000007.13, GRCh38); 1-based, inclusive interval notation.
- name: GRCh38 0-based, half-open interval notation
value: chr7:55259514-55259515
description: Genomic positions 55,259,514 to 55,259,515 on chromosome 1 (refseq:NC_000007.13, GRCh38); 0-based, half-open interval notation.
type: SequenceLocation
digest: LREsUiEYvOrRhwXW1rG72kXFPegvkNzI
sequenceReference:
id: refseq:NM_005228.5
name: NM_005228.5
description: The MANE Select (GRCh38) coding transcript for EGFR.
aliases:
- ensembl:ENST00000275493.7
- ga4gh:SQ.d_QsP29RWJi6bac7GOC9cJ9AO7s_HUMN
type: SequenceReference
refgetAccession: SQ.d_QsP29RWJi6bac7GOC9cJ9AO7s_HUMN
residueAlphabet: na
start: 2833
end: 2834
sequence: T
state:
type: LiteralSequenceExpression
sequence: G
- 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.g
value: NC_000007.13:g.55259515T>G
- syntax: hgvs.c
value: NM_005228.5:c.2573T>G
- syntax: hgvs.p
value: NP_005219.2:p.Leu858Arg
location:
id: ga4gh:SL.v0_edynH98OIu-0QPVT5anCSOriAFSDQ
description: Amino acid position 858 of the RefSeq protein NP_005219.2, which is the protein product of the MANE Select (GRCh38) coding transcript for EGFR (refseq:NM_005228.5).
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