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NM_000059.4(BRCA2):c.4819A>G (p.Ile1607Val) AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Jun 17, 2024
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:
RCV000657070.5

Allele description [Variation Report for NM_000059.4(BRCA2):c.4819A>G (p.Ile1607Val)]

NM_000059.4(BRCA2):c.4819A>G (p.Ile1607Val)

Gene:
BRCA2:BRCA2 DNA repair associated [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
13q13.1
Genomic location:
Preferred name:
NM_000059.4(BRCA2):c.4819A>G (p.Ile1607Val)
HGVS:
  • NC_000013.11:g.32339174A>G
  • NG_012772.3:g.28695A>G
  • NM_000059.4:c.4819A>GMANE SELECT
  • NP_000050.2:p.Ile1607Val
  • NP_000050.3:p.Ile1607Val
  • LRG_293t1:c.4819A>G
  • LRG_293:g.28695A>G
  • LRG_293p1:p.Ile1607Val
  • NC_000013.10:g.32913311A>G
  • NM_000059.3:c.4819A>G
Nucleotide change:
5047A>G
Protein change:
I1607V
Links:
dbSNP: rs200582465
NCBI 1000 Genomes Browser:
rs200582465
Molecular consequence:
  • NM_000059.4:c.4819A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000279511GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Uncertain significance
(Jun 17, 2024)
germlineclinical testing

Citation Link,

SCV000591928Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Uncertain significanceunknownclinical testing

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000279511.11

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis indicates that this missense variant does not alter protein structure/function; Also known as 5047A>G; This variant is associated with the following publications: (PMID: 31825140, 32467295, 27157322, 33471991, 14973102, 35300142)

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

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV000591928.2

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

Description

The BRCA2 p.Ile1607Val variant was identified by Suter (2004) in a healthy control subject, but was not identified in any of the breast cancer affected probands from this study. The variant was listed in the UMD as an unclassified variant in one sample. It was identified in dbSNP (ID: rs200582465) “With allele of Uncertain significance”, with a minor allele frequency of 0.0005 (1000 Genomes Project); however, this is based on only one observation of the variant allele. The variant was not listed in any of the other databases searched, including HGMD, COSMIC, LOVD and BIC. This residue is not conserved in mammals or lower organisms and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM) do not suggest a high likelihood of impact to the protein. However, this information is not predictive enough to rule out pathogenicity. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of unknown significance.

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

Last Updated: Sep 16, 2024