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NM_000059.4(BRCA2):c.3417G>A (p.Lys1139=)

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Interpretation:
Likely benign​

Review status:
reviewed by expert panel
Submissions:
8 (Most recent: Mar 31, 2021)
Last evaluated:
Jun 29, 2017
Accession:
VCV000135796.12
Variation ID:
135796
Description:
single nucleotide variant
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NM_000059.4(BRCA2):c.3417G>A (p.Lys1139=)

Allele ID
139508
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
13q13.1
Genomic location
13: 32337772 (GRCh38) GRCh38 UCSC
13: 32911909 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000013.11:g.32337772G>A
NG_012772.3:g.27293G>A
NM_000059.4:c.3417G>A MANE Select NP_000050.3:p.Lys1139= synonymous
... more HGVS
Protein change
-
Other names
p.K1139K:AAG>AAA
Canonical SPDI
NC_000013.11:32337771:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Trans-Omics for Precision Medicine (TOPMed) 0.00009
The Genome Aggregation Database (gnomAD), exomes 0.00016
Exome Aggregation Consortium (ExAC) 0.00011
Links
ClinGen: CA017974
dbSNP: rs145625991
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 reviewed by expert panel Jun 29, 2017 RCV000495720.3
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Nov 27, 2019 RCV000123962.6
Likely benign 2 criteria provided, multiple submitters, no conflicts Oct 1, 2015 RCV000162706.2
Benign 1 criteria provided, single submitter Jan 16, 2018 RCV000755222.4
Benign 1 criteria provided, single submitter Dec 6, 2020 RCV001083643.2
Likely benign 1 no assertion criteria provided - RCV001353513.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
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 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: SCV000579107.2
Submitted: (Jun 29, 2017)
Evidence details
Comment:
Synonymous substitution variant, with low bioinformatic likelihood to result in a splicing aberration (Splicing prior probability 0.02; http://priors.hci.utah.edu/PRIORS/).
Benign
(Feb 07, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000167354.11
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)
Likely benign
(Jul 14, 2014)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000213166.4
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
(Dec 06, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary breast and ovarian cancer syndrome
Allele origin: germline
Invitae
Accession: SCV000166165.11
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Oct 01, 2015)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000683554.1
Submitted: (Oct 26, 2017)
Evidence details
Benign
(Jan 16, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000602810.2
Submitted: (Oct 10, 2018)
Evidence details
Likely benign
(Nov 27, 2019)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000916995.2
Submitted: (Mar 06, 2020)
Evidence details
Publications
PubMed (1)
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
Malignant tumor of breast
Allele origin: unknown
Department of Pathology and Laboratory Medicine,Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV000591859.2
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The BRCA2 p.Lys1139= variant was identified in 1 of 4206 proband chromosomes (frequency: 0.0002) from individuals or families with breast cancer (Borg_2010_20104584). The variant was … (more)

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

Text-mined citations for rs145625991...

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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