NM_000059.4(BRCA2):c.10222A>T (p.Lys3408Ter) AND not specified

Clinical significance:Uncertain significance (Last evaluated: Jan 12, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_000059.4(BRCA2):c.10222A>T (p.Lys3408Ter)]

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

BRCA2:BRCA2 DNA repair associated [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_000059.4(BRCA2):c.10222A>T (p.Lys3408Ter)
Other names:
  • NC_000013.11:g.32398735A>T
  • NG_012772.3:g.88256A>T
  • NM_000059.3:c.10222A>T
  • NM_000059.4:c.10222A>TMANE SELECT
  • NP_000050.2:p.Lys3408Ter
  • NP_000050.3:p.Lys3408Ter
  • LRG_293t1:c.10222A>T
  • LRG_293:g.88256A>T
  • LRG_293p1:p.Lys3408Ter
  • NC_000013.10:g.32972872A>T
  • U43746.1:n.10450A>T
  • p.K3408*
  • p.Lys3408*
  • p.Lys3408Stop
Protein change:
dbSNP: rs80358402
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_000059.3:c.10222A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_000059.4:c.10222A>T - nonsense - [Sequence Ontology: SO:0001587]


MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000918936Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Uncertain significance
(Jan 12, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000918936.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided


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 cause nonsense-mediated decay. Truncations downstream of this position have not been classified as pathogenic by our laboratory and others in ClinVar. This variant was found in 3/296594 control chromosomes (gnomAD and FLOSSIES db) at a frequency of 0.0000101, which does not exceed the estimated maximal expected allele frequency of a pathogenic BRCA2 variant (0.0007503). The BRCA2 c.9976A>T (p.Lys3326*) variant, located upstream of this variant and also in the last exon of the gene, is a known benign variant suggesting that the truncation of the last 93 amino acids of BRCA2 is unlikely to be pathogenic for breast and/or ovarian cancer. The variant of interest has not, to our knowledge, been reported in affected individuals via publications. Multiple clinical diagnostic laboratories have recently classified this variant as likely benign (4), benign (1) or uncertain significance (1). Taken together this variant is classified as Variant of Unknown Significance-Possibly Benign.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 27, 2021

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