NM_000059.4(BRCA2):c.3479G>A (p.Arg1160Lys) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jun 27, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000521196.6

Allele description [Variation Report for NM_000059.4(BRCA2):c.3479G>A (p.Arg1160Lys)]

NM_000059.4(BRCA2):c.3479G>A (p.Arg1160Lys)

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.3479G>A (p.Arg1160Lys)

HGVS:

NC_000013.11:g.32337834G>A
NG_012772.3:g.27355G>A
NM_000059.4:c.3479G>AMANE SELECT
NP_000050.2:p.Arg1160Lys
NP_000050.3:p.Arg1160Lys
LRG_293t1:c.3479G>A
LRG_293:g.27355G>A
LRG_293p1:p.Arg1160Lys
NC_000013.10:g.32911971G>A
NM_000059.3:c.3479G>A

Nucleotide change:

3707G>A

Protein change:

R1160K

Links:

dbSNP: rs183920365

NCBI 1000 Genomes Browser:

rs183920365

Molecular consequence:

NM_000059.4:c.3479G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000616971	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Jun 27, 2023)	germline	clinical testing	Citation Link,
SCV001133755	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Uncertain significance (Feb 1, 2023)	unknown	clinical testing	PubMed (4) [See all records that cite these PMIDs] 31658756, 23096355, 27656653, 26467025

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000616971

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Jun 27, 2023)

germline

clinical testing

Citation Link,

SCV001133755

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Uncertain significance
(Feb 1, 2023)

unknown

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Landscape of Germline Mutations in DNA Repair Genes for Breast Cancer in Latin America: Opportunities for PARP-Like Inhibitors and Immunotherapy.

Urbina-Jara LK, Rojas-Martinez A, Martinez-Ledesma E, Aguilar D, Villarreal-Garza C, Ortiz-Lopez R.

Genes (Basel). 2019 Oct 10;10(10). doi:pii: E786. 10.3390/genes10100786. Review.

PubMed [citation]

PMID:: 31658756
PMCID:: PMC6827033

BRCA1 and BRCA2 mutations in breast cancer patients from Venezuela.

Lara K, Consigliere N, Pérez J, Porco A.

Biol Res. 2012;45(2):117-30. doi: 10.4067/S0716-97602012000200003.

PubMed [citation]

PMID:: 23096355

See all PubMed Citations (4)

Details of each submission

From GeneDx, SCV000616971.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Also known as 3707G>A; Observed in individuals with a personal and/or family history of breast cancer (Lara et al., 2012; Urbina-Jara et al., 2019); This variant is associated with the following publications: (PMID: 27656653, 31911673, 29884841, 32377563, 31658756, 33281875, 23096355, 30630528)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV001133755.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

The frequency of this variant in the general population, 0.00028 (10/35430 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. To the best of our knowledge, the variant has not been reported in individuals with a BRCA2 related disorder in the published literature. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is benign. Based on the available information, we are unable to determine the clinical significance of this variant.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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