13-32362694-G-A

Position:

• chr13-32362694-G-A

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1_Moderate PM2 PP5_Very_Strong

The NM_000059.4(BRCA2):​c.7976+1G>A variant causes a splice donor, intron change involving the alteration of a 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, intron
• Clinical Significance: Pathogenic reviewed by expert panel P:10
• Conservation: PhyloP100: 9.89

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]

BRCA2 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 12 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
• PP5: Variant 13-32362694-G-A is Pathogenic according to our data. Variant chr13-32362694-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 52452.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32362694-G-A is described in Lovd as [Pathogenic]. Variant chr13-32362694-G-A is described in Lovd as [Likely_pathogenic]. Variant chr13-32362694-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.7976+1G>A		splice_donor_variant, intron_variant		ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8	c.7976+1G>A		splice_donor_variant, intron_variant		5	NM_000059.4	ENSP00000369497.3
BRCA2	ENST00000530893.7	c.7607+1G>A		splice_donor_variant, intron_variant		1		ENSP00000499438.2
BRCA2	ENST00000614259.2	n.*34+1G>A		splice_donor_variant, intron_variant		2		ENSP00000506251.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:10

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge	Oct 02, 2015	- -
Pathogenic, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA2)	Feb 20, 2013	- -
Pathogenic, reviewed by expert panel	curation	Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)	Jun 18, 2019	IARC class based on posterior probability from multifactorial likelihood analysis, thresholds for class as per Plon et al. 2008 (PMID: 18951446). Class 5 based on posterior probability = 0.999776 -
Pathogenic, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Nov 19, 2010	- -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Aug 20, 2022	Canonical splice site variant demonstrated to result in the in-frame deletion of exon 17, impacting BRCA2 function (Wu 2005, Fraile-Bethencourt 2017); Not observed at significant frequency in large population cohorts (gnomAD); Also known as c.8204+1G>A; This variant is associated with the following publications: (PMID: 27157322, 18703817, 31131967, 29922827, 25525159, 17851763, 28339459, 29969168, 28993434, 29446198, 31825140, 30702160, 30078507, 32665702, 15695382) -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Apr 01, 2024	BRCA2: PVS1, PM2, PS4:Moderate -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Jul 06, 2023	The c.7976+1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide after coding exon 16 of the BRCA2 gene. This alteration has been detected in multiple breast cancer families (Palma MD et al. Cancer Res. 2008 Sep 1;68(17):7006-14; Li WF et al. Breast Cancer Res Treat. 2008 Jul;110(1):99-109). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. A minigene assay demonstrated that this alteration results in complete skipping of coding exon 16 (designated as exon 17 by the authors) (Fraile-Bethencourt E et al. PLoS Genet. 2017 Mar;13(3):e1006691). RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). In addition to the clinical and experimental data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as a disease-causing mutation. -
Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jul 22, 2020	This variant causes a G>A change at the +1 position in intron 17 of the BRCA2 gene. Functional RNA studies have shown that this variant and a similar splice site variant, c.7976+2C>G, resulted in the skipping of exon 17 and exons 17 and 18, causing the partial deletion of the DNA binding/OB tower domain of the BRCA2 protein and a frameshift, respectively (PMID: 28339459, 31843900). The in-frame deleted protein region contains 5 pathogenic missense variants reported in ClinVar (variation ID: 52423, 38125, 52430, 52455, 38131), which suggests that this region may be functionally important. The variant is expected to result in an absent or non-functional protein product. This variant has been reported in individuals affected with breast cancer and a family with strong history of breast/ovarian cancer (PMID: 17851763, 18703817, 31131967). 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. Based on available evidence, this variant is classified as Pathogenic. -

Hereditary breast ovarian cancer syndrome Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Oct 30, 2020	The c.7976+1G>A variant in BRCA2 has been reported in at least 6 individuals with BRCA2-associated cancers (Li 2018 PMID: 30078507, Wen 2018 PMID:28993434, additional studies summarized in Bhaskaran 2019 PMID: 30702160). Additionally, it was identified in several "high risk" individuals with a personal or family history of BRCA1/2 associated cancers that have undergone clinical genetic testing (Palma 2008 PMID: 18703817, Kwong 2016 PMID: 26187060, Rebbeck 2018 PMID: 29446198). It was absent from large population studies. This variant occurs within the canonical splice site (+/- 1,2) and is predicted to cause altered splicing leading to an abnormal or absent protein. In vitro functional studies show that this variant causes skipping of exon 17 leading to an in-frame deletion of 56 amino acids (Fraile-Bethencourt 2017 PMID: 28339459) that represents less than 10% of the BRCA2 protein. This variant was classified as pathogenic on June 18, 2019 by the ClinGen-approved ENIGMA expert panel (SCV001161564.1). In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal dominant HBOC. ACMG/AMP Criteria applied: PVS1_Moderate, PS4_Moderate, PM2_Supporting, PS3_Supporting. -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 12, 2023	This sequence change affects a donor splice site in intron 17 of the BRCA2 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and likely results in a shortened protein product. This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with or at high risk of breast and/or ovarian cancer (PMID: 17851763, 18703817, 22970155, 28993434, 29446198). ClinVar contains an entry for this variant (Variation ID: 52452). Studies have shown that disruption of this splice site results in skipping of exon 17, but is expected to preserve the integrity of the reading-frame (PMID: 28339459, 31191615; Invitae). This variant disrupts a region of the BRCA2 protein in which other variant(s) (p.Leu2653Pro) have been determined to be pathogenic (PMID: 22678057, 29061967; Invitae). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.44	D
BayesDel_noAF	Pathogenic	0.39
CADD	Pathogenic	32
DANN	Uncertain	1.0
Eigen	Pathogenic	1.3
Eigen_PC	Pathogenic	1.2
FATHMM_MKL	Pathogenic	0.98	D
GERP RS		5.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.93		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.93		Position offset: -1

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

Publications

LitVar

Other links and lift over

dbSNP: rs81002873; hg19: chr13-32936831; COSMIC: COSV66457548; COSMIC: COSV66457548;