rs81002798

chr13-32370558-G-Achr13-32370558-G-Cchr13-32370558-G-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1_Moderate PM2 PP3_Strong PP5_Very_Strong

The NM_000059.4(BRCA2):c.8487+1G>A variant causes a splice donor change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,457,402 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: BRCA2 NM_000059.4 splice_donor
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic reviewed by expert panel P:16 O:1
• Conservation: PhyloP100: 9.92

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 16 ACMG points.

• PVS1: Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 0.015111631 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: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 13-32370558-G-A is Pathogenic according to our data. Variant chr13-32370558-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 52602.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32370558-G-A is described in Lovd as [Pathogenic]. Variant chr13-32370558-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA2	NM_000059.4	c.8487+1G>A		splice_donor_variant		ENST00000380152.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA2	ENST00000380152.8	c.8487+1G>A		splice_donor_variant		5	NM_000059.4	A2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.86e-7 AC: 1 AN: 1457402 Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1 AN XY: 725408

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.03e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:16 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:5

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, 2004	- -
Pathogenic, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Nov 30, 2012	- -
Pathogenic, criteria provided, single submitter	clinical testing	Counsyl	Mar 30, 2018	- -
Pathogenic, reviewed by expert panel	curation	Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)	Aug 10, 2015	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 = 1 -

Hereditary breast ovarian cancer syndrome Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jun 05, 2018	Variant summary: BRCA2 c.8487+1G>A 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. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a 5' splicing donor site. At least two publications report experimental evidence supporting these predictions, which causes skipping of exon 19 leading to an abnormal protein product (p.Ille2778_Gln2829del)(Chen_2006, Agata_2003). The variant was absent in 276832 control chromosomes. c.8487+1G>A has been reported in the literature in multiple individuals affected with Hereditary Breast and Ovarian Cancer, indicating the variant is very likely to be associated with disease. Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, no assertion criteria provided	research	Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto	Jan 31, 2014	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Feb 08, 2016	The c.8487+1G>A variant in BRCA2 has been reported in at least 9 individuals wit h BRCA2-associated cancers (Chen 2006, Veschi 2007,Breast Cancer Information Cor e (BIC) database), and was absent from large population studies. This variant oc curs in the invariant region (+/- 1,2) of the splice consensus sequence and is p redicted to cause altered splicing leading to an abnormal or absent protein. In vitro functional studies provide evidence that the c.8487+1G>A variant impacts s plicing (Agata 2003, Acedo 2012, Chen 2006). Heterozygous loss of BRCA2 function is an established disease mechanism in hereditary breast and ovarian cancer (HB OC). Furthermore, this variant was classified as Pathogenic on August 10, 2015 b y the ClinGen-approved ENIGMA expert panel (ClinVar SCV000244485.1). In summary, this variant meets our criteria to be classified as pathogenic for HBOC in an a utosomal dominant manner based upon absence from controls, functional evidence, and predicted impact to the protein. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Dec 03, 2023	This sequence change affects a donor splice site in intron 19 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 breast cancer and/or ovarian cancer (PMID: 12606139, 16619214, 17591842, 24156927). This variant is also known as IVS19+1G>A. ClinVar contains an entry for this variant (Variation ID: 52602). Based on a multifactorial likelihood algorithm using genetic, in silico, and/or statistical data, this variant has been determined to have a high probability of being pathogenic (PMID: 17924331, 21990134, 25085752). Studies have shown that disruption of this splice site results in skipping of exon 19, but is expected to preserve the integrity of the reading-frame (PMID: 12606139, 16619214, 22632462; Invitae). This variant disrupts a region of the BRCA2 protein in which other variant(s) (p.Gly2793Arg) have been determined to be pathogenic (PMID: 12442275, 15889636, 16030099, 23108138, 23233716, 25085752, 25777348). 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. -

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	May 12, 2021	This variant is located in a canonical splice-donor site and interferes with normal BRCA2 mRNA splicing. The variant has been described in individuals with breast cancer in the published literature (PMID: 30702160 (2019), 29446198 (2018), 28294317 (2017), 27062684 (2016), 26681312 (2015), 24156927 (2014)). In addition, this variant has been shown to result in BRCA2 exon 19 skipping and the deletion of 52 amino acids from the BRCA2 protein ((PMID: 32398771 (2020), 22632462 (2012), 16619214 (2006)). This variant has not been reported in large, multi-ethnic general populations. Based on the available information, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Sep 27, 2021	The BRCA2 c.8487+1G>A variant (rs81002798), also known as IVS19+1, is reported in the literature in several individuals and families affected with breast and/or ovarian cancer (Agata 2003, Chen 2006, Gao 2020, Veschi 2007). This variant is also reported in ClinVar (Variation ID: 52602), and is classified as pathogenic by the evidence-based network for the interpretation of germline mutant alleles (ENIGMA) expert panel (see link to ENIGMA consortium classification criteria). This variant is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. This variant disrupts the canonical splice donor site of intron 19, and functional assays demonstrate skipping of exon 19 (Agata 2003, Chen 2006). Based on available information, this variant is considered to be pathogenic. References: Link to ENIGMA classification criteria: https://enigmaconsortium.org/library/general-documents/enigma-classification-criteria/ Agata S et al. The BRCA2 sequence variant IVS19+1G-->A leads to an aberrant transcript lacking exon 19. Cancer Genet Cytogenet. 2003 Mar;141(2):175-6. PMID: 12606139. Chen X et al. Intronic alterations in BRCA1 and BRCA2: effect on mRNA splicing fidelity and expression. Hum Mutat. 2006 May;27(5):427-35. PMID: 16619214. Gao X et al. Comprehensive profiling of BRCA1 and BRCA2 variants in breast and ovarian cancer in Chinese patients. Hum Mutat. 2020 Mar;41(3):696-708. PMID: 31825140. Veschi S et al. High prevalence of BRCA1 deletions in BRCAPRO-positive patients with high carrier probability. Ann Oncol. 2007 Jun;18 Suppl 6:vi86-92. PMID: 17591842. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Feb 08, 2022	Canonical splice site variant demonstrated to result in an in-frame deletion of the critical DSS1 contacting residues of the DNA binding domain (Yang 2002, Agata 2003, Chen 2006, Acedo 2012); Observed in multiple individuals with a personal and/or family history of breast and/or ovarian cancer (Agata 2003, Chen 2006, Veschi 2007, Tea 2014, Lang 2017); Multifactorial studies suggest this variant is associated with breast and ovarian cancer (Lindor 2012); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Not observed in large population cohorts (gnomAD); Also known as 8715+1G>A; This variant is associated with the following publications: (PMID: 17591842, 26681312, 24728327, 21990134, 12606139, 22632462, 17924331, 16619214, 27060066, 24156927, 25085752, 29446198, 29061375, 31209999, 25525159, 32398771, 30787465, 31825140, 30702160, 28294317, 12228710) -

Hereditary cancer-predisposing syndrome Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Mar 11, 2021	The c.8487+1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide after coding exon 18 of the BRCA2 gene. This mutation has been reported in multiple individuals with personal and/or family histories consistent with hereditary breast and ovarian cancer (HBOC) syndrome (Agata S et al. Cancer Genet. Cytogenet. 2003 Mar;141:175-6; Chen X et al. Hum. Mutat. 2006 May;27:427-35; Susswein LR et al. Genet. Med. 2016 Aug;18:823-32). Multiple splicing assays have shown that this alteration leads to complete skipping of coding exon 18, resulting in a predicted in-frame deletion of 52 amino acid residues in a functionally important region of the BRCA2 protein (Ambry internal data; Mesman RLS et al. Genet Med 2020 08;22(8):1355-1365; Chen X et al. Hum. Mutat. 2006 May;27:427-35; Acedo A et al. Breast Cancer Res. 2012 May 25;14:R87; Agata S et al. Cancer Genet. Cytogenet. 2003 Mar;141:175-6). In addition to the clinical 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	curation	Sema4, Sema4	Sep 20, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Nov 22, 2021	This variant causes a G to A nucleotide substitution at the +1 position of intron 19 of the BRCA2 gene. It is also known as IVS19+1G>A in the literature. Functional RNA studies have shown that this variant results in the skipping of exon 19, causing an in-frame deletion of 52 amino acids within the essential DNA binding domain of BRCA2 protein (PMID: 12606139, 16619214, 22632462). This variant has been reported in individuals affected with breast and/or ovarian cancer (PMID: 16619214, 24156927, 28423363; Color internal data). Multifactorial likelihood analyses based on genetic data using personal/family history, co-segregation, and co-occurrence predict that this variant has a high probability of being deleterious (PMID: 17924331, 21990134, 25085752). 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. -

Familial cancer of breast Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Sep 21, 2023

- -

not specified Other:1

not provided, no classification provided

reference population

ITMI

Sep 19, 2013

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.44	D
BayesDel_noAF	Pathogenic	0.40
Cadd	Pathogenic	32
Dann	Uncertain	1.0
Eigen	Pathogenic	1.2
Eigen_PC	Pathogenic	1.0
FATHMM_MKL	Pathogenic	0.99	D
MutationTaster	Benign	1.0	D;D
GERP RS		5.2

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		0.96		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.96		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: rs81002798; hg19: chr13-32944695;