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NM_000059.4(BRCA2):c.4850G>A (p.Ser1617Asn)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(3);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Sep 25, 2021)
Last evaluated:
Sep 3, 2021
Accession:
VCV000037928.12
Variation ID:
37928
Description:
single nucleotide variant
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NM_000059.4(BRCA2):c.4850G>A (p.Ser1617Asn)

Allele ID
46484
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
13q13.1
Genomic location
13: 32339205 (GRCh38) GRCh38 UCSC
13: 32913342 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_000059.3:c.4850G>A NP_000050.2:p.Ser1617Asn missense
LRG_293:g.28726G>A
LRG_293t1:c.4850G>A LRG_293p1:p.Ser1617Asn
... more HGVS
Protein change
S1617N
Other names
5078G>A
Canonical SPDI
NC_000013.11:32339204:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00000
Exome Aggregation Consortium (ExAC) 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD) 0.00001
Links
ClinGen: CA020915
dbSNP: rs397507341
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 criteria provided, multiple submitters, no conflicts Sep 10, 2018 RCV000166443.3
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Aug 4, 2021 RCV000697920.5
Uncertain significance 2 criteria provided, single submitter Sep 3, 2021 RCV000437440.5
Likely benign 1 criteria provided, single submitter Apr 5, 2018 RCV001703438.1
Likely benign 1 no assertion criteria provided Oct 4, 2010 RCV000031509.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
BRCA2 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
13784 13899

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jun 13, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000217238.4
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign);Other data supporting benign classification
Uncertain significance
(Mar 11, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary breast and ovarian cancer syndrome
Allele origin: germline
Invitae
Accession: SCV000826554.4
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change replaces serine with asparagine at codon 1617 of the BRCA2 protein (p.Ser1617Asn). The serine residue is weakly conserved and there is a … (more)
Likely benign
(Apr 05, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000520481.4
Submitted: (Sep 25, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 21232165, 21120943)
Uncertain significance
(Sep 03, 2021)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001442544.2
Submitted: (Nov 10, 2020)
Evidence details
Publications
PubMed (4)
Comment:
Variant summary: BRCA2 c.4850G>A (p.Ser1617Asn) results in a conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a benign … (more)
Likely benign
(Sep 10, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000906092.1
Submitted: (Nov 06, 2018)
Evidence details
Uncertain significance
(Aug 04, 2021)
criteria provided, single submitter
Method: clinical testing
Hereditary breast and ovarian cancer syndrome
Allele origin: germline
St. Jude Clinical Genomics Lab, St. Jude Children's Research Hospital
Accession: SCV000890913.2
Submitted: (Aug 07, 2021)
Evidence details
Likely benign
(Oct 04, 2010)
no assertion criteria provided
Method: clinical testing
Breast-ovarian cancer, familial 2
Allele origin: germline
Sharing Clinical Reports Project (SCRP)
Accession: SCV000054114.4
Submitted: (Aug 22, 2012)
Evidence details
Uncertain significance
(Jan 31, 2014)
no assertion criteria provided
Method: research
not specified
Allele origin: germline
Research Molecular Genetics Laboratory,Women's College Hospital, University of Toronto
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV000587727.1
Submitted: (Aug 04, 2017)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Breast Cancer Risk Genes - Association Analysis in More than 113,000 Women. Breast Cancer Association Consortium. The New England journal of medicine 2021 PMID: 33471991
A Bayesian framework for efficient and accurate variant prediction. Qian D PloS one 2018 PMID: 30212499
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
The occurrence of germline BRCA1 and BRCA2 sequence alterations in Slovenian population. Stegel V BMC medical genetics 2011 PMID: 21232165
EMMA, a cost- and time-effective diagnostic method for simultaneous detection of point mutations and large-scale genomic rearrangements: application to BRCA1 and BRCA2 in 1,525 patients. Caux-Moncoutier V Human mutation 2011 PMID: 21120943

Text-mined citations for rs397507341...

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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 Nov 27, 2021