NM_000059.4(BRCA2):c.8702G>A (p.Gly2901Asp) AND not provided

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Feb 3, 2021
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:: RCV000590249.15

Allele description [Variation Report for NM_000059.4(BRCA2):c.8702G>A (p.Gly2901Asp)]

NM_000059.4(BRCA2):c.8702G>A (p.Gly2901Asp)

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.8702G>A (p.Gly2901Asp)

Other names:

p.G2901D:GGT>GAT

HGVS:

NC_000013.11:g.32376739G>A
NG_012772.3:g.66260G>A
NM_000059.4:c.8702G>AMANE SELECT
NP_000050.2:p.Gly2901Asp
NP_000050.3:p.Gly2901Asp
LRG_293t1:c.8702G>A
LRG_293:g.66260G>A
LRG_293p1:p.Gly2901Asp
NC_000013.10:g.32950876G>A
NM_000059.3:c.8702G>A
U43746.1:n.8930G>A
p.G2901D

Nucleotide change:

8930G>A

Protein change:

G2901D

Links:

dbSNP: rs80359129

NCBI 1000 Genomes Browser:

rs80359129

Molecular consequence:

NM_000059.4:c.8702G>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
SCV000210479	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Feb 3, 2021)	germline	clinical testing	Citation Link,
SCV000695176	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely benign (May 2, 2016)	germline	clinical testing	PubMed (10) [See all records that cite these PMIDs] 26221963, 26757417, 26848529, 9579822, 22486713, 18779604, 23108138, 14973102, 18627636, 18607349 LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV001133946	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Benign (Sep 7, 2018)	germline	clinical testing	PubMed (12) [See all records that cite these PMIDs] 18607349, 19043619, 9579822, 18627636, 22486713, 23108138, 26757417, 28222693, 29394989, 29681614, 18779604, 26467025

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000210479

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(Feb 3, 2021)

germline

clinical testing

Citation Link,

SCV000695176

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely benign
(May 2, 2016)

germline

clinical testing

PubMed (10)
[See all records that cite these PMIDs]

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV001133946

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Benign
(Sep 7, 2018)

germline

clinical testing

PubMed (12)
[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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Predictive Factors for BRCA1 and BRCA2 Genetic Testing in an Asian Clinic-Based Population.

Wong ES, Shekar S, Chan CH, Hong LZ, Poon SY, Silla T, Lin C, Kumar V, Davila S, Voorhoeve M, Thike AA, Ho GH, Yap YS, Tan PH, Tan MH, Ang P, Lee AS.

PLoS One. 2015;10(7):e0134408. doi: 10.1371/journal.pone.0134408.

PubMed [citation]

PMID:: 26221963
PMCID:: PMC4519264

Prevalence and spectrum of BRCA germline variants in mainland Chinese familial breast and ovarian cancer patients.

Kim YC, Zhao L, Zhang H, Huang Y, Cui J, Xiao F, Downs B, Wang SM.

Oncotarget. 2016 Feb 23;7(8):9600-12. doi: 10.18632/oncotarget.7144.

PubMed [citation]

PMID:: 26848529
PMCID:: PMC4891063

See all PubMed Citations (15)

Details of each submission

From GeneDx, SCV000210479.12

#	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: 26757417, 23108138, 19043619, 28277317, 14973102, 18607349, 9579822, 24323938, 22486713, 18627636, 18779604, 26221963, 11251181, 28222693, 29394989, 26848529, 29681614, 24817641, 31131967, 29884841, 31825140)

#	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 Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000695176.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (10)

Description

Variant summary: The c.8702G>A variant affects a conserved nucleotide, resulting in amino acid change from Gly to Asp. 4/4 in-silico tools predict damaging outcome for this variant. This variant is found in 14/121646 control chromosomes from ExAC at a frequency of 0.0001151. It was predominantly reported in East Asian subpopulation with an allele frequency of 0.0016 which is about 2.15 times higher than the maximum expected allele frequency of a pathogenic variant in this gene suggesting that it is likely to be a polymorphism in East Asians. The variant has been reported in several breast and/or ovarian cancer patients/families, mainly of East Asian origin, without strong evidence for pathogenicity. In one patient with thyroid and breast cancer, a truncating mutation PTEN c. 590delA was also found, possibly suggesting for an alternative disease mechanism. In addition, it was also found in once in each of benign breast cancer patient and healthy control cohorts, possibly suggesting a benign outcome. Functional studies (HDR, cell viability and drug sensitivity assays) shows neutral outcome for this variant. Three out of five clinical labs have also classified this variant as likely benign/benign (other two as uncertain significance). Taken together, this variant has currently been classified as likely benign.

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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV001133946.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (12)

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

Last Updated: Nov 3, 2024

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