13-32362695-C-G

Position:

• chr13-32362695-C-G

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1_Moderate PM2 PP3_Moderate PP5_Very_Strong

The NM_000059.4(BRCA2):​c.7976+2C>G variant causes a splice donor change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: BRCA2 NM_000059.4 splice_donor
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:6
• Conservation: PhyloP100: 3.39

Genes affected

BRCA2 (HGNC:1101): (BRCA2 DNA repair associated) Inherited mutations in BRCA1 and this gene, BRCA2, confer increased lifetime risk of developing breast or ovarian cancer. Both BRCA1 and BRCA2 are involved in maintenance of genome stability, specifically the homologous recombination pathway for double-strand DNA repair. The largest exon in both genes is exon 11, which harbors the most important and frequent mutations in breast cancer patients. The BRCA2 gene was found on chromosome 13q12.3 in human. The BRCA2 protein contains several copies of a 70 aa motif called the BRC motif, and these motifs mediate binding to the RAD51 recombinase which functions in DNA repair. BRCA2 is considered a tumor suppressor gene, as tumors with BRCA2 mutations generally exhibit loss of heterozygosity (LOH) of the wild-type allele. [provided by RefSeq, May 2020]

ACMG classification

Verdict is Pathogenic. Variant got 14 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.016574048 fraction of the gene. No cryptic splice site detected. Exon removal is inframe change.
• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 13-32362695-C-G is Pathogenic according to our data. Variant chr13-32362695-C-G is described in ClinVar as [Pathogenic]. Clinvar id is 418088.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA2	NM_000059.4	c.7976+2C>G		splice_donor_variant		ENST00000380152.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA2	ENST00000380152.8	c.7976+2C>G		splice_donor_variant		5	NM_000059.4	A2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Aug 24, 2018	This pathogenic variant is denoted BRCA2 c.7976+2C>G or IVS17+2C>G and consists of a C>G nucleotide substitution at the +2 position of intron 17 of the BRCA2 gene. Using alternate nomenclature, this variant would be defined as BRCA2 8204+2C>G. This variant destroys a canonical splice donor site and is predicted to cause abnormal gene splicing, leading to an abnormal message that is subject to nonsense-mediated mRNA decay or to an abnormal protein product. It would be predicted to result in an in-frame deletion of the adjacent exon 17, and loss of exon 17 has been demonstrated to disrupt BRCA2 protein function (Wu 2005). BRCA2 c.7976+2C>G has been reported in at least one individual referred for BRCA1/2 testing (Costa 2013). Based on currently available evidence, we consider this variant to be pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Feb 13, 2023	This variant disrupts a canonical splice-donor site and interferes with normal BRCA2 mRNA splicing. A functional RNA study reported this variant results in skipping of exon 17 or exon 17 and 18 (PMID: 31843900 (2019)). This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). In the published literature, the variant has been reported in a family with two individuals affected with breast cancer (PMID: 31528241 (2019)). Based on the available information, this variant is classified as pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jul 24, 2022	This variant causes a C>G nucleotide substitution at the +2 position of intron 17 of the BRCA2 gene. An RNA study has shown that this variant resulted in primarily the in-frame skipping of exon 17 that partially encodes the DNA binding domain and a minor product with out-of-frame skipping of exons 17 and 18 (PMID: 31843900). Exon 17 includes five codons that have pathogenic missense variants reported in ClinVar (variation ID: 52423, 38125, 52430, 52455, 38131), which suggests that the exon 17 encoded region may be functionally important. To our knowledge, functional studies have not been performed for this variant. This variant has been reported in an individual affected with cancer from a family severely affected with cancers of the breast, ovary, endometrium, or colon (PMID: 31843900) and another individual affected with early-onset breast cancer with family history of the disease (PMID: 31528241). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of BRCA2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Oct 28, 2021	The c.7976+2C>G intronic pathogenic mutation results from a C to G substitution two nucleotides after coding exon 16 in the BRCA2 gene. This nucleotide position is well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data; Casadei S et al. Proc Natl Acad Sci U S A, 2019 Dec;). Several other alterations impacting the same donor site (BRCA2 c.7976+5G>A, BRCA2 c.7976+5G>T, BRCA2 c.7976G>A) has been shown to have a similar impact on splicing in (Casadei S et al. Proc Natl Acad Sci U S A, 2019 Dec; Wong MS et al. Mol Cell, 2018 09;71:1012-1026.e3; Montalban G et al. Hum Mutat, 2018 09;39:1155-1160). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Hereditary breast ovarian cancer syndrome;C2675520:Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:1

Pathogenic, no assertion criteria provided

research

King Laboratory, University of Washington

Sep 01, 2019

- -

Hereditary breast ovarian cancer syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

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

Dec 16, 2021

Variant summary: BRCA2 c.7976+2C>G is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. One computational tool predicts a significant impact on normal splicing through abolishing of 5' splicing donor site. Impact on splicing has been confirmed by experimental evidence demonstrating skipping of exon 17, or both exons 17 and 18 (Casadei_2019). The variant was absent in 251134 control chromosomes (gnomAD), and c.7976+2C>G has been reported in the literature in at least one family affected with Hereditary Breast And Ovarian Cancer Syndrome (Casadei_2019). Three ClinVar submitters have assessed this variant since 2014: all have classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.22	D
BayesDel_noAF	Uncertain	0.070
CADD	Uncertain	24
DANN	Benign	0.95
Eigen	Pathogenic	0.89
Eigen_PC	Pathogenic	0.70
FATHMM_MKL	Uncertain	0.89	D
MutationTaster	Benign	1.0	D;D
GERP RS		3.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.83		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.83		Position offset: -2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs886040943; hg19: chr13-32936832;