NM_000059.4(BRCA2):c.2919G>A (p.Ser973=) AND Breast-ovarian cancer, familial, susceptibility to, 2

Germline classification:: Benign (5 submissions)
Last evaluated:: Jun 29, 2017
Review status:: 3 stars out of maximum of 4 stars
reviewed by expert panel

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:: RCV000113113.13

Allele description [Variation Report for NM_000059.4(BRCA2):c.2919G>A (p.Ser973=)]

NM_000059.4(BRCA2):c.2919G>A (p.Ser973=)

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.2919G>A (p.Ser973=)

Other names:

S973S; p.S973S:TCG>TCA; NP_000050.3:p.Ser973=

HGVS:

NC_000013.11:g.32337274G>A
NG_012772.3:g.26795G>A
NM_000059.4:c.2919G>AMANE SELECT
NP_000050.2:p.Ser973=
NP_000050.3:p.Ser973=
LRG_293t1:c.2919G>A
LRG_293:g.26795G>A
LRG_293p1:p.Ser973=
NC_000013.10:g.32911411G>A
NM_000059.3:c.2919G>A
NM_000059.4:c.2919G>A
U43746.1:n.3147G>A
p.S973S

Links:

dbSNP: rs45525041

NCBI 1000 Genomes Browser:

rs45525041

Molecular consequence:

NM_000059.4:c.2919G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Name:: Breast-ovarian cancer, familial, susceptibility to, 2 (BROVCA2)
Synonyms:: Breast-ovarian cancer, familial 2
Identifiers:: MONDO: MONDO:0012933; MedGen: C2675520; Orphanet: 145; OMIM: 612555

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Phytophthora infestans T30-4 supercont1.9 genomic scaffold, whole genome shotgun sequence
gi|301113142|ref|NW_003303750.1||gn _WGS:AATU|supercont1.9

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000146139	Breast Cancer Information Core (BIC) (BRCA2)	no assertion criteria provided	Uncertain significance (Jan 24, 2003)	germline	clinical testing
SCV000220910	Counsyl	criteria provided, single submitter (Counsyl Autosomal Dominant Disease Classification criteria (2015))	Likely benign (Nov 24, 2014)	unknown	literature only	PubMed (4) [See all records that cite these PMIDs] 17453335, 15172753, 20041885, 20104584 Counsyl Autosomal Dominant Disease Classification criteria (2015), Citation Link,
SCV000383663	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 28, 2017)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 17453335, 26306726, 24814045, 15172753, 20041885 Citation Link,
SCV000578022	Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)	reviewed by expert panel (ENIGMA BRCA1/2 Classification Criteria (2017-06-29))	Benign (Jun 29, 2017)	germline	curation	Citation Link,
SCV004243597	BRCAlab, Lund University	no assertion criteria provided	Benign (Mar 2, 2020)	germline	clinical testing

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, curation
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	literature only
Caucasian	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Characterization of BRCA1 and BRCA2 deleterious mutations and variants of unknown clinical significance in unilateral and bilateral breast cancer: the WECARE study.

Borg A, Haile RW, Malone KE, Capanu M, Diep A, Törngren T, Teraoka S, Begg CB, Thomas DC, Concannon P, Mellemkjaer L, Bernstein L, Tellhed L, Xue S, Olson ER, Liang X, Dolle J, Børresen-Dale AL, Bernstein JL.

Hum Mutat. 2010 Mar;31(3):E1200-40. doi: 10.1002/humu.21202.

PubMed [citation]

PMID:: 20104584
PMCID:: PMC2928257

Greek BRCA1 and BRCA2 mutation spectrum: two BRCA1 mutations account for half the carriers found among high-risk breast/ovarian cancer patients.

Konstantopoulou I, Rampias T, Ladopoulou A, Koutsodontis G, Armaou S, Anagnostopoulos T, Nikolopoulos G, Kamakari S, Nounesis G, Stylianakis A, Karanikiotis C, Razis E, Gogas H, Keramopoulos A, Gaki V, Markopoulos C, Skarlos D, Pandis N, Bei T, Arzimanoglou I, Fountzilas G, Yannoukakos D.

Breast Cancer Res Treat. 2008 Feb;107(3):431-41. Epub 2007 Apr 24.

PubMed [citation]

PMID:: 17453335

See all PubMed Citations (6)

Details of each submission

From Breast Cancer Information Core (BIC) (BRCA2), SCV000146139.1

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

#	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		1	not provided	not provided	not provided

From Counsyl, SCV000220910.2

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

#	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

From Illumina Laboratory Services, Illumina, SCV000383663.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is 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 Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA), SCV000578022.2

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

Description

Synonymous substitution variant, with low bioinformatic likelihood to alter mRNA splicing (splicing prior 0.02; http://priors.hci.utah.edu/PRIORS/) and frequency 0.0018 (South Asian), derived from ExAC (2014-12-17).

#	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 BRCAlab, Lund University, SCV004243597.1

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

#	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

Last Updated: Oct 20, 2024

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