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NM_007294.4(BRCA1):c.5152+20T>A

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
9 (Most recent: Sep 21, 2021)
Last evaluated:
Dec 31, 2019
Accession:
VCV000132704.10
Variation ID:
132704
Description:
single nucleotide variant
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NM_007294.4(BRCA1):c.5152+20T>A

Allele ID
136452
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q21.31
Genomic location
17: 43063854 (GRCh38) GRCh38 UCSC
17: 41215871 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000017.10:g.41215871A>T
NC_000017.11:g.43063854A>T
NG_005905.2:g.154130T>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000017.11:43063853:A:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (T)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00009
The Genome Aggregation Database (gnomAD) 0.00013
1000 Genomes Project 0.00020
Trans-Omics for Precision Medicine (TOPMed) 0.00008
Exome Aggregation Consortium (ExAC) 0.00009
Trans-Omics for Precision Medicine (TOPMed) 0.00014
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015
The Genome Aggregation Database (gnomAD), exomes 0.00016
Links
ClinGen: CA003282
dbSNP: rs376836050
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, multiple submitters, no conflicts Jun 20, 2019 RCV000123931.5
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Oct 15, 2015 RCV000130822.4
Likely benign 2 criteria provided, multiple submitters, no conflicts May 28, 2019 RCV000411645.2
Benign 1 criteria provided, single submitter Dec 31, 2019 RCV000119141.11
Likely benign 1 no assertion criteria provided - RCV001689666.1
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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
12040 12208

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary breast and ovarian cancer syndrome
Allele origin: germline
Invitae
Accession: SCV000153856.11
Submitted: (Jan 29, 2020)
Evidence details
Likely benign
(Jun 01, 2016)
criteria provided, single submitter
Method: clinical testing
Breast-ovarian cancer, familial 1
Allele origin: unknown
Counsyl
Accession: SCV000487762.1
Submitted: (Nov 23, 2016)
Evidence details
Publications
PubMed (1)
Benign
(May 09, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000167318.11
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
(Dec 05, 2013)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000185718.2
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
(Oct 15, 2015)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000683260.1
Submitted: (Oct 26, 2017)
Evidence details
Benign
(Jun 20, 2019)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000918724.2
Submitted: (Sep 24, 2019)
Evidence details
Publications
PubMed (3)
Comment:
Variant summary: BRCA1 c.5152+20T>A alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly … (more)
Likely benign
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Breast-ovarian cancer, familial 1
Allele origin: unknown
Mendelics
Accession: SCV001140485.1
Submitted: (Oct 22, 2019)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics Laboratory, Department of Pathology,Netherlands Cancer Institute
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001905997.1
Submitted: (Sep 20, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001973823.1
Submitted: (Sep 21, 2021)
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
A simple method for co-segregation analysis to evaluate the pathogenicity of unclassified variants; BRCA1 and BRCA2 as an example. Mohammadi L BMC cancer 2009 PMID: 19563646
Diagnostic guidelines for high-resolution melting curve (HRM) analysis: an interlaboratory validation of BRCA1 mutation scanning using the 96-well LightScanner. van der Stoep N Human mutation 2009 PMID: 19370767
Denaturing high-performance liquid chromatography detects reliably BRCA1 and BRCA2 mutations. Wagner T Genomics 1999 PMID: 10644434

Text-mined citations for rs376836050...

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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