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NM_000059.4(BRCA2):c.9411T>G (p.Thr3137=)

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Interpretation:
Benign​

Review status:
reviewed by expert panel
Submissions:
7 (Most recent: Sep 24, 2021)
Last evaluated:
Jun 29, 2017
Accession:
VCV000183987.11
Variation ID:
183987
Description:
single nucleotide variant
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NM_000059.4(BRCA2):c.9411T>G (p.Thr3137=)

Allele ID
184074
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
13q13.1
Genomic location
13: 32394843 (GRCh38) GRCh38 UCSC
13: 32968980 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000013.10:g.32968980T>G
LRG_293:g.84364T>G
LRG_293t1:c.9411T>G LRG_293p1:p.Thr3137=
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000013.11:32394842:T:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00005
The Genome Aggregation Database (gnomAD) 0.00047
The Genome Aggregation Database (gnomAD) 0.00076
Exome Aggregation Consortium (ExAC) 0.00052
Trans-Omics for Precision Medicine (TOPMed) 0.00003
The Genome Aggregation Database (gnomAD), exomes 0.00055
Links
ClinGen: CA026146
dbSNP: rs1799968
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 reviewed by expert panel Jun 29, 2017 RCV000494944.3
Likely benign 2 criteria provided, multiple submitters, no conflicts Jan 13, 2017 RCV000163082.2
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Sep 7, 2021 RCV000588721.4
Benign 1 criteria provided, single submitter Nov 13, 2020 RCV001082585.2
Likely benign 1 criteria provided, single submitter Aug 30, 2019 RCV001287804.2
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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
Benign
(Jun 29, 2017)
reviewed by expert panel
Method: curation
Breast-ovarian cancer, familial 2
Allele origin: germline
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)
Accession: SCV000578020.2
Submitted: (Jun 29, 2017)
Evidence details
Comment:
Synonymous substitution variant, with low bioinformatic likelihood to alter mRNA splicing (splicing prior 0.02; http://priors.hci.utah.edu/PRIORS/) and frequency 0.0033 (Finnish), derived from ExAC (2014-12-17).
Likely benign
(Nov 20, 2014)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000213585.4
Submitted: (Nov 30, 2020)
Evidence details
Comment:
This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, … (more)
Benign
(Nov 13, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary breast and ovarian cancer syndrome
Allele origin: germline
Invitae
Accession: SCV000253060.7
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jan 13, 2017)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000689194.1
Submitted: (Dec 21, 2017)
Evidence details
Benign
(May 18, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000695238.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (4)
Comment:
Variant summary: The BRCA2 c.9411T>G (p.Thr3137Thr) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a … (more)
Likely benign
(Aug 30, 2019)
criteria provided, single submitter
Method: clinical testing
none provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001474534.1
Submitted: (Dec 11, 2020)
Evidence details
Likely benign
(Sep 07, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000516027.4
Submitted: (Sep 24, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 10399947, 9150152, 9585608, 20104584)

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
Characterization of BRCA1 and BRCA2 deleterious mutations and variants of unknown clinical significance in unilateral and bilateral breast cancer: the WECARE study. Borg A Human mutation 2010 PMID: 20104584
Germline brca2 sequence variants in patients with ocular melanoma. Sinilnikova OM International journal of cancer 1999 PMID: 10399947
Evidence of founder mutations in Finnish BRCA1 and BRCA2 families. Huusko P American journal of human genetics 1998 PMID: 9585608
A low proportion of BRCA2 mutations in Finnish breast cancer families. Vehmanen P American journal of human genetics 1997 PMID: 9150152

Text-mined citations for rs1799968...

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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 Dec 04, 2021