Submissions for variant NM_000059.4(BRCA2):c.9501+3A>T

gnomAD frequency: 0.00008  dbSNP: rs61757642

Total submissions: 32

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)	RCV000031825	SCV001161629	benign	Breast-ovarian cancer, familial, susceptibility to, 2	2019-06-18	reviewed by expert panel	curation	IARC class based on posterior probability from multifactorial likelihood analysis, thresholds for class as per Plon et al. 2008 (PMID: 18951446). Class 1 based on posterior probability = 4.85E-07
Labcorp Genetics (formerly Invitae), Labcorp	RCV000167798	SCV000073851	benign	Hereditary breast ovarian cancer syndrome	2024-02-01	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV000131261	SCV000186226	likely benign	Hereditary cancer-predisposing syndrome	2019-03-08	criteria provided, single submitter	clinical testing	This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Michigan Medical Genetics Laboratories, University of Michigan	RCV000031825	SCV000196027	uncertain significance	Breast-ovarian cancer, familial, susceptibility to, 2	2014-11-03	criteria provided, single submitter	clinical testing
GeneDx	RCV000656812	SCV000210508	uncertain significance	not provided	2017-09-05	criteria provided, single submitter	clinical testing	This variant is denoted BRCA2 c.9501+3A>T or IVS25+3A>T and consists of an A>T nucleotide substitution at the +3 position of intron 25 of the BRCA2 gene. This variant, also known as 9729+3A>T using alternate nomenclature, has been observed in breast and/or ovarian cancer families (Capalbo 2006, Papi 2009, Borg 2010, Gabald? Barrios 2017). In vitro and in vivo RNA studies report that BRCA2 c.9501+3A>T results in skipping of exon 25 (Bonnet 2008, Papi 2009, Borg 2010, Whiley 2011). In addition, the Evidence-Based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) Splicing Working Group concluded that BRCA2 c.9501+3A>T produces unequivocal splicing aberrations (Whiley 2014). However, a minigene splicing assay quantified the aberrant splicing and found that this variant results in less than 15% aberrant transcript, meaning that the full length transcript is predominant (Acedo 2015). Additionally, the adenine (A) nucleotide that is altered is not conserved. BRCA2 c.9501+3A>T was observed at an allele frequency of 0.02% (16/66,618) in individuals of European (Non-Finnish) ancestry in large population cohorts (Lek 2016). Despite BRCA2 c.9501+3A>T being proven to result in skipping of exon 25, we are unable to predict the clinical impact of this variant given that the normal transcript appears to be more abundant. Thus, we consider it to be a variant of uncertain significance.
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000656812	SCV000296748	benign	not provided	2023-07-26	criteria provided, single submitter	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000031825	SCV000743367	likely benign	Breast-ovarian cancer, familial, susceptibility to, 2	2014-10-09	criteria provided, single submitter	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000031825	SCV000744565	likely benign	Breast-ovarian cancer, familial, susceptibility to, 2	2017-05-31	criteria provided, single submitter	clinical testing
Mendelics	RCV000167798	SCV000838906	benign	Hereditary breast ovarian cancer syndrome	2023-08-22	criteria provided, single submitter	clinical testing
Color Diagnostics, LLC DBA Color Health	RCV000131261	SCV000902673	likely benign	Hereditary cancer-predisposing syndrome	2022-05-10	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000045838	SCV000918821	benign	not specified	2022-12-12	criteria provided, single submitter	clinical testing	Variant summary: BRCA2 c.9501+3A>T alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Three predict the variant weakens a canonical 5' donor site and one predicts the variant abolishes a canonical 5' splicing donor site. These predictions are supported by multiple functional studies that showed exon 25 was skipped (e.g. Bonnet_2008). However, several of these studies found that only a small fraction of transcript skipped exon 25, thereby calling into question the clinical relevance of the variant (e.g. Acedo_2014). In further contrast, a recently published study evaluating RNA genetic testing to re-classify splice variants has reported that this variant has no impact on splicing in accordance with the ACMG BS3 gudeline specification supporting its re-classification as likely benign (Karam_2019). The variant allele was found at a frequency of 0.00012 in 251052 control chromosomes, predominantly at a frequency of 0.0002 within the Non-Finnish European subpopulation in the gnomAD database. This frequency is not higher than expected for a pathogenic variant in BRCA2 causing Hereditary Breast And Ovarian Cancer Syndrome (0.00012 vs 0.00075), allowing no conclusion about variant significance. 6 heterozygous European American women over the age of 70 with no history of cancer (carrier frequency = 0.0008191) were found in a seperate dataset (FLOSSIES). c.9501+3A>T has been reported in the literature in individuals affected with breast cancer (e.g. Capalbo_2006, Whiley_2011, van der Hout_2006, Pajares_2018). In a recent report from Caputo_2021, the authors assigned an IARC classification of "1-benign" to the variant from their multifactorial likelihood analysis which incorporated co-segregation data from several unrelated French families. Multiple co-occurrences with other pathogenic variants have been reported in the UMD database and also observed in our laboratory and the literature (examples, UMD-BRCA2 c.5796_5797delTA, p.His1932GlnfsX12; BRCA2 c.2957dup, p.Asn986LysfsX2; BRCA1 c.1266T>G, p.Tyr422X; our laboratory-BRCA1 c.5153-2del; Karam_2019, an unspecified observation in trans with a pathogenic mutation in an individual without biallelic disease), providing supporting evidence for a benign role. Sixteen ClinVar submitters, including one expert panel (ENIGMA), have assessed the variant since 2014: nine classified the variant as uncertain significance, five as likely benign, and two as benign. Among these, the expert panel settled on a benign classification. Based on the evidence outlined above, the variant was classified as benign.
CeGaT Center for Human Genetics Tuebingen	RCV000656812	SCV001249504	uncertain significance	not provided	2021-02-01	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000031825	SCV001267537	uncertain significance	Breast-ovarian cancer, familial, susceptibility to, 2	2017-04-27	criteria provided, single submitter	clinical testing	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. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000656812	SCV001473401	likely benign	not provided	2021-09-09	criteria provided, single submitter	clinical testing
Mayo Clinic Laboratories, Mayo Clinic	RCV000656812	SCV001714442	uncertain significance	not provided	2019-08-17	criteria provided, single submitter	clinical testing
National Health Laboratory Service, Universitas Academic Hospital and University of the Free State	RCV000167798	SCV002504871	uncertain significance	Hereditary breast ovarian cancer syndrome	2022-04-19	criteria provided, single submitter	clinical testing
Genetics Program, Instituto Nacional de Cancer	RCV000167798	SCV002515166	likely benign	Hereditary breast ovarian cancer syndrome	2021-11-01	criteria provided, single submitter	research
Fulgent Genetics, Fulgent Genetics	RCV002504848	SCV002798780	benign	Familial cancer of breast; Breast-ovarian cancer, familial, susceptibility to, 2; Fanconi anemia complementation group D1; Medulloblastoma; Wilms tumor 1; Malignant tumor of prostate; Pancreatic cancer, susceptibility to, 2; Glioma susceptibility 3	2022-03-30	criteria provided, single submitter	clinical testing
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000045838	SCV004027492	benign	not specified	2023-08-15	criteria provided, single submitter	clinical testing
Sharing Clinical Reports Project (SCRP)	RCV000031825	SCV000054433	benign	Breast-ovarian cancer, familial, susceptibility to, 2	2011-09-16	no assertion criteria provided	clinical testing
Breast Cancer Information Core (BIC) (BRCA2)	RCV000031825	SCV000147652	uncertain significance	Breast-ovarian cancer, familial, susceptibility to, 2	2002-05-29	no assertion criteria provided	clinical testing
Laboratoire de Biologie et Génétique du Cancer, Centre François Baclesse	RCV000031825	SCV000538194	uncertain significance	Breast-ovarian cancer, familial, susceptibility to, 2		no assertion criteria provided	clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV000656812	SCV000592289	uncertain significance	not provided		no assertion criteria provided	clinical testing	The BRCA2 c.9501+3A>T variant was identified in 3 of 4414 proband chromosomes (frequency: 0.001) from individuals or families with breast/ovarian cancers in 2 studies (Borg 2010, Papi 2009). Giannini et al. (2006) also identified the variant in an Italian cohort of breast/ovarian cancer families, frequency unspecified. Multiple functional assays using minigene reporters and/or RNA analysis have shown that the variant causes incomplete skipping of exon 25, with wildtype transcript present and the splicing alteration affecting only a fraction of the transcripts from the variant allele (Bonnet 2008, Whiley 2011, Acedo 2015, Houdayer 2012). The variant was also identified in dbSNP (ID: rs61757642) “With likely pathogenic allele”, in the Exome Variant Server project in 3 of 8600 European American alleles (frequency: 0.0003), the Exome Aggregation Consortium (ExAC) database (released Jan 13, 2015) in 18 of 121142 chromosomes (frequency: 0.0001) (or 16 individuals from a population of European (Non-Finnish) individuals and 2 individuals from a population of Latinos). It was also identified by our laboratory in 7 individuals with breast and ovarian cancer co-occuring with BRCA2 c.9976A>T in at least 3 individuals. The variant was identified in the Clinvitae database (4x), ARUP Laboratories BRCA Mutations Database (classification pathogenic), the ClinVar database with conflicting interpretations (classified as a benign variant by the Sharing Clinical Reports Project, derived from Myriad reports; classified as likely pathogenic by GeneDX and CHEO, and uncertain significance by Ambry Genetics, BIC and Invitae), GeneInsight COGR database (2x, classified as “likely pathogenic” and unclassified), the BIC database (15x with unknown clinical importance and pending classification), UMD (classified as likely casual 15x, including 1x co-occuring with a pathogenic mutation c.5796_5797delTA (p.His1932GlnfsX12)). The c.9501+3A>T variant is located in the 5' splice region but does not affect the invariant +1 and +2 positions. However, positions +3 to +6 are part of the splicing consensus sequence and variants involving these positions sometimes affect splicing. In addition, 4 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of unknown significance.
Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research	RCV000735627	SCV000863765	uncertain significance	Breast and/or ovarian cancer	2013-08-23	no assertion criteria provided	clinical testing
Hereditary Cancer Genetics group, Vall d'Hebron Institute of Oncology	RCV000167798	SCV000916375	uncertain significance	Hereditary breast ovarian cancer syndrome	2019-03-01	no assertion criteria provided	research
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000045838	SCV001744918	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute	RCV000656812	SCV001905877	likely benign	not provided		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000045838	SCV001951608	benign	not specified		no assertion criteria provided	clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	RCV000656812	SCV002035684	likely benign	not provided		no assertion criteria provided	clinical testing
Department of Medical and Surgical Sciences, University of Bologna	RCV000031825	SCV004228302	benign	Breast-ovarian cancer, familial, susceptibility to, 2	2023-09-01	no assertion criteria provided	clinical testing	BS1(Strong)+BP5(Very Strong) according to ACMG/AMP classification guidelines specified for BRCA1 & BRCA2 (Classification Criteria V1.0.0 2023-09-08 - https://cspec.genome.network/cspec/ui/svi/affiliation/50087) (PMID: 38160042)
BRCAlab, Lund University	RCV000031825	SCV004243873	benign	Breast-ovarian cancer, familial, susceptibility to, 2	2020-03-02	no assertion criteria provided	clinical testing
PreventionGenetics, part of Exact Sciences	RCV004541054	SCV004765970	likely benign	BRCA2-related disorder	2022-12-13	no assertion criteria provided	clinical testing	This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).