rs81002812

chr13-32379316-G-Achr13-32379316-G-Cchr13-32379316-G-T

Variant summary

Our verdict is Pathogenic. Variant got 22 ACMG points: 22P and 0B. PVS1 PM2 PP3_Strong PP5_Very_Strong

The NM_000059.4(BRCA2):c.8755-1G>A variant causes a splice acceptor change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,242 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/2 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: BRCA2 NM_000059.4 splice_acceptor
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic reviewed by expert panel P:25
• Conservation: PhyloP100: 7.91

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 22 ACMG points.

• PVS1: Splicing variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift 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. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 13-32379316-G-A is Pathogenic according to our data. Variant chr13-32379316-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 38183.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32379316-G-A is described in Lovd as [Pathogenic]. Variant chr13-32379316-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA2	NM_000059.4	c.8755-1G>A		splice_acceptor_variant		ENST00000380152.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA2	ENST00000380152.8	c.8755-1G>A		splice_acceptor_variant		5	NM_000059.4	A2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000205 AC: 3 AN: 1461242 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 726924

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: 0.00000270

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

Alfa AF: 0.000470 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:25

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:9

Likely pathogenic, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Apr 18, 2011	- -
Pathogenic, no assertion criteria provided	clinical testing	Institute of Human Genetics, Medical University Innsbruck	Feb 11, 2015	- -
Pathogenic, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA2)	Feb 20, 2004	- -
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, criteria provided, single submitter	research	Centre for Mendelian Genomics, University Medical Centre Ljubljana	Dec 09, 2022	PVS1, PS3, PS4_STR, PM2_SUP, PP1 -
Likely pathogenic, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine	Feb 05, 2019	This c.8755-1G>A variant in the BRCA2 gene has been shown to alter mRNA splicing and is predicted to introduce a premature translation termination codon (PMID 18489799, 23451180, 25382762). This variant has been reported in multiple families affected with hereditary breast and ovarian cancer (PMID 18489799, 24156927) and has never been observed in general population databases. Therefore, the c.8755-1G>A variant is classified as pathogenic. -
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 = 0.999891 -
Likely pathogenic, criteria provided, single submitter	literature only	Counsyl	Sep 03, 2014	- -

not provided Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Jan 30, 2023	PP5, PM2, PVS1 -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jan 12, 2023	Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; Observed in individuals with a personal or family history consistent with pathogenic variants in this gene (Wagner et al., 1999; Tea et al., 2014; Lerner-Ellis et al., 2021; Solao et al., 2021); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Not observed at significant frequency in large population cohorts (gnomAD); Also known as 8983-1G>A; This variant is associated with the following publications: (PMID: 23199084, 31131967, 29785153, 23451180, 9971877, 18489799, 25382762, 24156927, 23772696, 27060066, 20104584, 28726806, 29360161, 30257646, 29387975, 29446198, 29922827, 28918466, 32206145, 32885271, 32438681, 35264596, 24312913, 34072659, Eniu2017[Abstract]) -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

Hereditary breast ovarian cancer syndrome Pathogenic:4

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	Invitae	Dec 28, 2023	This sequence change affects an acceptor splice site in intron 21 of the BRCA2 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted 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 personal and/or family history of breast and/or ovarian cancer (PMID: 9971877, 18489799, 24156927). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 38183). Studies have shown that disruption of this splice site alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 9971877, 23451180, 25382762). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Sep 19, 2017	Variant summary: The BRCA2 c.8755-1G>A variant involves the alteration of a conserved intronic nucleotide and 3/5 splice prediction tools predict a significant impact on normal splicing. A functional study, Colombo_2013, shows the variant to produce two aberrant transcripts, skipping of exon 22 (resulting in p.Gly2919LeufsX3) and skipping of exon 22 + 51 bp at the 5' end of exon 23 (resulting in p.Gly2919LysfsX26). This variant is absent in 244786 control chromosomes (gnomAD). A publication, Tea_2014, reports the variant in 26 affected individuals from 13 families. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as "Pathogenic." Taken together, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Dec 22, 2015	The c.8755-1G>A variant in BRCA2 has been reported in at least 10 individuals wi th BRCA2-associated cancers and segregated with disease in 3 affected relatives from 3 families (Wagner 1999, Machackova 2008, Breast Cancer Information Core da tabase, www.research.nhgri.nih.gov/bic/). It was absent from large population st udies. This variant occurs in the invariant region (+/- 1,2) of the splice conse nsus sequence and in vitro studies indicate that this variant results in skippin g of exon 22, leading to a premature stop codon and an abnormal or absent protei n (Machackova 2008, Colombo 2013). Heterozygous loss of function of the BRCA2 ge ne is an established disease mechanism in hereditary breast and ovarian cancer ( HBOC). In summary, this variant meets our criteria to be classified as pathogeni c for HBOC in an autosomal dominant manner based upon the predicted impact to th e protein, segregation studies, and prevalence in affected individuals. -

Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Department of Molecular Diagnostics, Institute of Oncology Ljubljana	Apr 02, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Mar 08, 2023	_x000D_ Criteria applied: PVS1, PS3_MOD, PS4_MOD, PM2_SUP -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jan 29, 2021	This variant causes a G to A nucleotide substitution at the canonical -1 position of intron 21 splice acceptor site of the BRCA2 gene. This variant is also known as IVS21-1G>A in the literature. Functional RNA studies have shown that this variant causes skipping of exon 22 or skipping of exon 22 plus first 51 nucleotides of exon 23 (PMID: 9971877, 18489799, 23451180, 25382762). This variant is expected to result in an absent or non-functional protein product. This variant has been reported in over fifteen individuals affected with breast and/or ovarian cancer (PMID: 9971877, 11802209, 18489799, 29785153, 32206145, 32438681; Matteis 2019, DOI: 10.12892/ejgo5165.2019) and in an individual affected with pancreatic and prostate cancer with family history of breast and/or ovarian cancer (PMID: 29360161). This variant has also been reported in 26 individuals from 13 different families at high risk for breast cancer (PMID: 24156927). 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	Nov 11, 2021	The c.8755-1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide upstream from coding exon 21 of the BRCA2 gene. This alteration has been identified in multiple individuals with a personal and/or family history of breast and/or ovarian cancer (Machackova E et al. BMC Cancer. 2008 May;8:140; Tea MK et al. Maturitas. 2014 Jan;77:68-72; Goidescu IG et al. Clujul Med, 2018 Apr;91:157-165; Boltear L et al. Hered Cancer Clin Pract, 2020 Mar;18:7). This alteration has also been reported in 1 of 1296 individuals with pancreatic adenocarcinoma (Dudley B et al. Cancer, 2018 Apr;124:1691-1700). In multiple RNA studies, transcript analysis and minigene assays revealed aberrant transcripts that can lead to a frameshift as the result of this alteration (Ambry internal data; Colombo M et al. PLoS ONE. 2013 Mar;8(2):e57173; Acedo A et al. Hum. Mutat. 2015 Feb;36(2):210-21). 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. -

not specified Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneKor MSA

Jul 01, 2016

- -

Carcinoma of pancreas Pathogenic:1

Pathogenic, no assertion criteria provided

case-control

CZECANCA consortium

Mar 04, 2021

- -

Malignant tumor of breast Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The BRCA2 c.8755-1G>A variant was identified in the literature however the frequency of this variant in an affected population was not provided. The variant was also identified in dbSNP (ID: rs81002812) as With Likely pathogenic, Pathogenic allele, ClinVar (classified as pathogenic by Invitae, Ambry Genetics, BIC; classified as likely pathogenic by SCRP, Counsyl; classified as uncertain significance by ENIGMA ), Clinvitae (conflicting interpretations of pathogenicity), Genesight-COGR, LOVD 3.0 , UMD-LSDB (2X causal), BIC Database (6X clinically important), ARUP Laboratories (Definitely pathogenic), databases. The variant was not identified in Zhejiang Colon Cancer Database, databases. The variant was not identified in the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project or the Exome Aggregation Consortium (August 8th 2016) control databases. The c.8755-1G>A variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the invariant region of the splice consensus sequence. In addition, 2 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. Several functional studies using splicing assays demonstrated the variant result in aberrant transcripts and considered as deleterious mutations (Acedo 2015, Machackova 2008). mRNA Transcript Analysis in in vitro study by Colombo (2012) showed skipping of exon 22 in one case and skipping of exon 22+51 bp at the 59-end of exon 23 in another. In the same study, cDNA sequence analyses revealed maintenance of the constitutional heterozygosity for c.9876G>A synonymous change (exon 27), indicating expression of the normal mRNA from both the wild-type and mutated alleles. In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. -

Familial cancer of breast Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Apr 04, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.40	D
BayesDel_noAF	Pathogenic	0.34
Cadd	Pathogenic	35
Dann	Uncertain	0.99
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.92
FATHMM_MKL	Pathogenic	0.98	D
MutationTaster	Benign	1.0	D;D
GERP RS		5.6

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.94
SpliceAI score (max)		0.99		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.95		Position offset: 2
DS_AL_spliceai		0.99		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: rs81002812; hg19: chr13-32953453;