NM_000059.4(BRCA2):c.470_474del (p.Lys157fs) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 30, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV002293415.9

Allele description [Variation Report for NM_000059.4(BRCA2):c.470_474del (p.Lys157fs)]

NM_000059.4(BRCA2):c.470_474del (p.Lys157fs)

Gene:
BRCA2:BRCA2 DNA repair associated [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
13q13.1
Genomic location:
Preferred name:
NM_000059.4(BRCA2):c.470_474del (p.Lys157fs)
Other names:
698_702delAGTCA
HGVS:
  • NC_000013.10:g.32900281_32900285del
  • NC_000013.11:g.32326145_32326149del
  • NG_012772.3:g.15666_15670del
  • NM_000059.4:c.470_474delMANE SELECT
  • NM_000059.4:c.470_474delAGTCA
  • NP_000050.3:p.Lys157fs
  • LRG_293:g.15666_15670del
  • NC_000013.10:g.32900281_32900285del
  • NC_000013.10:g.32900282_32900286del
  • NC_000013.10:g.32900282_32900286delAGTCA
  • NM_000059.3:c.470_474delAGTCA
  • NM_000059.4:c.470_474del
  • U43746.1:n.698_702delAGTCA
  • p.K157Sfs*24
  • p.Lys157Serfs*24
Nucleotide change:
698del5
Links:
Breast Cancer Information Core (BIC) (BRCA2): 698&base_change=del AGTCA; dbSNP: rs80359463
NCBI 1000 Genomes Browser:
rs80359463
Molecular consequence:
  • NM_000059.4:c.470_474del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002586839GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Pathogenic
(Mar 30, 2022) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV002586839.2

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

Description

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease, while also shown to result in aberrant splicing resulting in multiple transcripts including deletion exon 5 (Sanz 2010, Stauffer 2020); Observed in individuals with a personal or family history consistent with pathogenic variants in this gene (Li 2008, Cao 2016, Weren 2016, Sun 2017); Published functional studies demonstrate a damaging effect: reduced cell viability and hypersensitivity to DNA damaging agents (Stauffer 2020); Not observed at significant frequency in large population cohorts (gnomAD); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Also known as 698_702del or 469_473del; This variant is associated with the following publications: (PMID: 30720863, 28176296, 30702160, 31174498, 27060066, 29487695, 28294317, 26295337, 33563323, 32926049, 26852015, 32623769, 30883759, 31825140, 17851763, 20215541, 22632462, 32393813, 28724667, 27767231)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 8, 2024