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NM_000059.4(BRCA2):c.10222A>T (p.Lys3408Ter)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(5);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
9 (Most recent: Sep 29, 2021)
Last evaluated:
Nov 11, 2020
Accession:
VCV000051056.12
Variation ID:
51056
Description:
single nucleotide variant
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NM_000059.4(BRCA2):c.10222A>T (p.Lys3408Ter)

Allele ID
65724
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
13q13.1
Genomic location
13: 32398735 (GRCh38) GRCh38 UCSC
13: 32972872 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000013.10:g.32972872A>T
NM_000059.3:c.10222A>T NP_000050.2:p.Lys3408Ter nonsense
LRG_293:g.88256A>T
... more HGVS
Protein change
K3408*
Other names
p.K3408*:AAG>TAG
Canonical SPDI
NC_000013.11:32398734:A:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD) 0.00003
The Genome Aggregation Database (gnomAD) 0.00004
The Genome Aggregation Database (gnomAD), exomes 0.00000
Exome Aggregation Consortium (ExAC) 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00005
Links
ClinGen: CA010501
dbSNP: rs80358402
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 Mar 12, 2019 RCV000131732.6
Likely benign 2 criteria provided, multiple submitters, no conflicts Aug 30, 2019 RCV000759573.5
Benign 1 criteria provided, single submitter Nov 11, 2020 RCV000043728.3
Likely benign 3 criteria provided, single submitter Apr 5, 2017 RCV000112851.3
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV000212295.5
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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
(Mar 12, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000186772.5
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Other data supporting benign classification
Benign
(Nov 11, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary breast and ovarian cancer syndrome
Allele origin: germline
Invitae
Accession: SCV000071741.7
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000108594.12
Submitted: (Sep 29, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 10923033, 20104584)
Likely benign
(Feb 22, 2017)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000683399.1
Submitted: (Oct 26, 2017)
Evidence details
Likely benign
(Apr 05, 2017)
criteria provided, single submitter
Method: clinical testing
Breast-ovarian cancer, familial 2
Allele origin: unknown
Counsyl
Accession: SCV000785078.2
Submitted: (Jun 20, 2018)
Evidence details
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000918936.1
Submitted: (Apr 24, 2019)
Evidence details
Comment:
Variant summary: The BRCA2 c.10222A>T (p.Lys3408X) variant results in truncation of the last 10 amino acids in the last exon; therefore it is unexpected to … (more)
Likely benign
(Aug 30, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: unknown
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000888974.3
Submitted: (Dec 31, 2020)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
Breast-ovarian cancer, familial 2
Allele origin: germline
Breast Cancer Information Core (BIC) (BRCA2)
Accession: SCV000145768.1
Submitted: (Mar 28, 2014)
Evidence details
Uncertain significance
(-)
no assertion criteria provided
Method: clinical testing
Breast-ovarian cancer, familial 2
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: SCV000592318.2
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The p.Lys3408X variant was not identified in the literature but was identified in the BIC database (1X with no clinical importance), dbSNP (ID: rs80358402), and … (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
The breast cancer information core: database design, structure, and scope. Szabo C Human mutation 2000 PMID: 10923033

Text-mined citations for rs80358402...

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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