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NM_007294.4(BRCA1):c.5402G>A (p.Gly1801Asp)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Feb 9, 2021)
Last evaluated:
Jan 30, 2021
Accession:
VCV000142834.9
Variation ID:
142834
Description:
single nucleotide variant
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NM_007294.4(BRCA1):c.5402G>A (p.Gly1801Asp)

Allele ID
152548
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q21.31
Genomic location
17: 43049125 (GRCh38) GRCh38 UCSC
17: 41201142 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000017.10:g.41201142C>T
NC_000017.11:g.43049125C>T
NM_007294.4:c.5402G>A MANE Select NP_009225.1:p.Gly1801Asp missense
... more HGVS
Protein change
G1801D, G1754D, G1822D, G697D
Other names
p.G1801D:GGC>GAC
Canonical SPDI
NC_000017.11:43049124:C:T
Functional consequence
functionally_normal [Sequence Ontology SO:0002219]
The saturation genome editing (SGE) assay for BRCA1 NM_007294.3:c.5402G>A, a MISSENSE variant, produced a function score of 0.04, corresponding to a functional classification of FUNCTIONAL. SGE function score ranges for classification are as follows: ‘functional’, score > -0.748; ‘intermediate’, -0.748 > score > -1.328; ‘non-functional’, score < -1.328. The median synonymous SNV scored 0.0 and the median nonsense SNV scored -2.12. [submitted by Brotman Baty Institute,University of Washington]
Global minor allele frequency (GMAF)
0.00020 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00002
Exome Aggregation Consortium (ExAC) 0.00004
1000 Genomes Project 0.00020
Links
dbSNP: rs531210457
ClinGen: CA003552
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Jul 26, 2019 RCV000132269.4
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Jan 30, 2021 RCV000160007.4
Benign 1 criteria provided, single submitter Nov 23, 2020 RCV000461010.6
not provided 1 no assertion provided - RCV001073171.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
BRCA1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
12270 12437

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Apr 04, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000210218.9
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Jun 06, 2016)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000910793.1
Submitted: (Nov 06, 2018)
Evidence details
Likely benign
(Jul 26, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000187352.5
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign);Seen in trans with a mutation or in homozygous state in individual without severe disease for that gene
Benign
(Nov 23, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary breast and ovarian cancer syndrome
Allele origin: germline
Invitae
Accession: SCV000549327.6
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Benign
(Jan 30, 2021)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001337979.2
Submitted: (Feb 09, 2021)
Evidence details
Publications
PubMed (5)
Comment:
Variant summary: BRCA1 c.5402G>A (p.Gly1801Asp) results in a non-conservative amino acid change located in the BRCT domain (IPR001357) of the encoded protein sequence. Four of … (more)
not provided
(-)
no assertion provided
Method: in vitro
Breast-ovarian cancer, familial 1
Allele origin: not applicable
Brotman Baty Institute,University of Washington
Accession: SCV001238682.1
Submitted: (Nov 12, 2018)
Evidence details
Publications
PubMed (1)

Functional evidence

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Functional consequence Method Result Submitter Supporting information
functionally_normal
  1. saturation genome editing in haploid cells
  2. Method citation(s):
  1. FUNCTIONAL:0.042955773559517
Brotman Baty Institute,University of Washington
Accession: SCV001238682.1
Submitted: (Nov 12, 2018)
Evidence details
Publications
PubMed (1)
Comment:
The saturation genome editing (SGE) assay for BRCA1 NM_007294.3:c.5402G>A, a MISSENSE variant, produced a function score of 0.04, corresponding to a functional classification of FUNCTIONAL. … (more)

Citations for this variant

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Title Author Journal Year Link
Germline <i>BRCA1</i> and <i>BRCA2</i> deleterious mutations and variants of unknown clinical significance associated with breast/ovarian cancer: a report from North India. Mehta A Cancer management and research 2018 PMID: 30555256
Accurate classification of BRCA1 variants with saturation genome editing. Findlay GM Nature 2018 PMID: 30209399
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Genomic hallmarks of homologous recombination deficiency in invasive breast carcinomas. Manié E International journal of cancer 2016 PMID: 26317927
Patterns and functional implications of rare germline variants across 12 cancer types. Lu C Nature communications 2015 PMID: 26689913
BRCA1/BRCA2 gene mutations/SNPs and BRCA1 haplotypes in early-onset breast cancer patients of Indian ethnicity. Juwle A Medical oncology (Northwood, London, England) 2012 PMID: 22752604
https://sge.gs.washington.edu/BRCA1/ - - - -

Text-mined citations for rs531210457...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jun 14, 2021