NM_000059.4(BRCA2):c.10087A>G (p.Ile3363Val) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Sep 8, 2021
Review status:: criteria provided, conflicting classifications

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:: RCV000985457.7

Allele description [Variation Report for NM_000059.4(BRCA2):c.10087A>G (p.Ile3363Val)]

NM_000059.4(BRCA2):c.10087A>G (p.Ile3363Val)

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.10087A>G (p.Ile3363Val)

Other names:

p.I3363V:ATA>GTA

HGVS:

NC_000013.11:g.32398600A>G
NG_012772.3:g.88121A>G
NM_000059.4:c.10087A>GMANE SELECT
NP_000050.2:p.Ile3363Val
NP_000050.3:p.Ile3363Val
LRG_293t1:c.10087A>G
LRG_293:g.88121A>G
LRG_293p1:p.Ile3363Val
NC_000013.10:g.32972737A>G
NM_000059.3:c.10087A>G
p.I3363V

Protein change:

I3363V

Links:

dbSNP: rs55881945

NCBI 1000 Genomes Browser:

rs55881945

Molecular consequence:

NM_000059.4:c.10087A>G - 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
SCV000108593	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Nov 26, 2018)	germline	clinical testing	Citation Link,
SCV001133664	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Uncertain significance (Sep 8, 2021)	unknown	clinical testing	PubMed (4) [See all records that cite these PMIDs] 22034289, 26287763, 28301460, 26467025

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000108593

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(Nov 26, 2018)

germline

clinical testing

Citation Link,

SCV001133664

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Uncertain significance
(Sep 8, 2021)

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	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

High prevalence of BRCA1 and BRCA2 mutations in unselected Nigerian breast cancer patients.

Fackenthal JD, Zhang J, Zhang B, Zheng Y, Hagos F, Burrill DR, Niu Q, Huo D, Sveen WE, Ogundiran T, Adebamowo C, Odetunde A, Falusi AG, Olopade OI.

Int J Cancer. 2012 Sep 1;131(5):1114-23. doi: 10.1002/ijc.27326. Epub 2012 Jan 27.

PubMed [citation]

PMID:: 22034289

A high frequency of BRCA mutations in young black women with breast cancer residing in Florida.

Pal T, Bonner D, Cragun D, Monteiro AN, Phelan C, Servais L, Kim J, Narod SA, Akbari MR, Vadaparampil ST.

Cancer. 2015 Dec 1;121(23):4173-80. doi: 10.1002/cncr.29645. Epub 2015 Aug 19.

PubMed [citation]

PMID:: 26287763
PMCID:: PMC4666784

See all PubMed Citations (4)

Details of each submission

From GeneDx, SCV000108593.14

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

Description

This variant is associated with the following publications: (PMID: 22034289, 26287763)

#	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, SCV001133664.4

#	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 (7/24946 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported in individuals with breast cancer (PMIDs: 22034289 (2012) and 26287763 (2015)). 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: Apr 20, 2024

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