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NM_000059.4(BRCA2):c.167A>C (p.Asn56Thr)

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Interpretation:
Benign​

Review status:
reviewed by expert panel
Submissions:
8 (Most recent: Sep 24, 2021)
Last evaluated:
Aug 10, 2015
Accession:
VCV000037751.11
Variation ID:
37751
Description:
single nucleotide variant
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NM_000059.4(BRCA2):c.167A>C (p.Asn56Thr)

Allele ID
46307
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
13q13.1
Genomic location
13: 32319176 (GRCh38) GRCh38 UCSC
13: 32893313 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000013.11:g.32319176A>C
NG_012772.3:g.8697A>C
NG_017006.2:g.1188T>G
... more HGVS
Protein change
N56T
Other names
p.N56T:AAT>ACT
395A>C
Canonical SPDI
NC_000013.11:32319175:A:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00002
Exome Aggregation Consortium (ExAC) 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Links
ClinGen: CA012889
dbSNP: rs80358454
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 reviewed by expert panel Aug 10, 2015 RCV000031332.7
Likely benign 2 criteria provided, multiple submitters, no conflicts Jan 28, 2021 RCV000043861.12
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Jul 25, 2017 RCV000162996.2
Likely benign 1 criteria provided, single submitter Dec 4, 2020 RCV001084320.2
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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
13782 13897

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Aug 10, 2015)
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: SCV000244424.1
Submitted: (Aug 17, 2015)
Evidence details
Publications
PubMed (1)
Other databases
http://hci-exlovd.hci.utah.edu/v…
Comment:
IARC class based on posterior probability from multifactorial likelihood analysis, thresholds for class as per Plon et al. 2008 (PMID: 18951446). Class 1 based on … (more)
Likely benign
(Jul 25, 2017)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000903287.1
Submitted: (Nov 06, 2018)
Evidence details
Likely benign
(Jul 30, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000600482.2
Submitted: (Mar 06, 2020)
Evidence details
Publications
PubMed (4)
Likely benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary breast and ovarian cancer syndrome
Allele origin: germline
Invitae
Accession: SCV000071874.9
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Nov 19, 2014)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000213484.4
Submitted: (Nov 30, 2020)
Evidence details
Comment:
This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA … (more)
Likely benign
(Jan 28, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000210658.11
Submitted: (Sep 24, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 28866612, 24323938, 21952622, 21990134, 17924331, 26898890, 32123317)
Uncertain significance
(May 29, 2002)
no assertion criteria provided
Method: clinical testing
Breast-ovarian cancer, familial 2
Allele origin: germline
Breast Cancer Information Core (BIC) (BRCA2)
Accession: SCV000146286.1
Submitted: (Mar 28, 2014)
Evidence details
Likely benign
(Feb 09, 2011)
no assertion criteria provided
Method: clinical testing
Breast-ovarian cancer, familial 2
Allele origin: germline
Sharing Clinical Reports Project (SCRP)
Accession: SCV000053937.3
Submitted: (Jun 26, 2013)
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
Functional assays for analysis of variants of uncertain significance in BRCA2. Guidugli L Human mutation 2014 PMID: 24323938
A review of a multifactorial probability-based model for classification of BRCA1 and BRCA2 variants of uncertain significance (VUS). Lindor NM Human mutation 2012 PMID: 21990134
A systematic genetic assessment of 1,433 sequence variants of unknown clinical significance in the BRCA1 and BRCA2 breast cancer-predisposition genes. Easton DF American journal of human genetics 2007 PMID: 17924331
The breast cancer information core: database design, structure, and scope. Szabo C Human mutation 2000 PMID: 10923033
Incidence of BRCA1/2 germ line alterations in a high risk cohort participating in a phase II chemoprevention trial. Klemp J European journal of cancer (Oxford, England : 1990) 2000 PMID: 10882858
http://hci-exlovd.hci.utah.edu/variants.php?select_db=BRCA2&action=search_all&search_Variant%2FDNA=c.167A%3EC - - - -

Text-mined citations for rs80358454...

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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 20, 2021