rs61757642
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_000059.4(BRCA2):c.9501+3A>T variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000991 in 1,613,894 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★★).
Frequency
Genomes: 𝑓 0.000072 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00010 ( 0 hom. )
Consequence
BRCA2
NM_000059.4 splice_donor_region, intron
NM_000059.4 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.9886
1
1
Clinical Significance
Conservation
PhyloP100: 2.04
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
?
Variant 13-32394936-A-T is Benign according to our data. Variant chr13-32394936-A-T is described in ClinVar as [Benign]. Clinvar id is 38242.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32394936-A-T is described in Lovd as [Pathogenic]. Variant chr13-32394936-A-T is described in Lovd as [Likely_benign]. Variant chr13-32394936-A-T is described in Lovd as [Benign].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRCA2 | NM_000059.4 | c.9501+3A>T | splice_donor_region_variant, intron_variant | ENST00000380152.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRCA2 | ENST00000380152.8 | c.9501+3A>T | splice_donor_region_variant, intron_variant | 5 | NM_000059.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152228Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000116 AC: 29AN: 251052Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135712
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GnomAD4 exome AF: 0.000102 AC: 149AN: 1461666Hom.: 0 Cov.: 31 AF XY: 0.000102 AC XY: 74AN XY: 727120
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GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74384
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ClinVar
Significance: Benign
Submissions summary: Uncertain:11Benign:21
Revision: reviewed by expert panel
LINK: link
Submissions by phenotype
Breast-ovarian cancer, familial, susceptibility to, 2 Uncertain:4Benign:6
Benign, 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 1 based on posterior probability = 4.85E-07 - |
Uncertain significance, no assertion criteria provided | clinical testing | Breast Cancer Information Core (BIC) (BRCA2) | May 29, 2002 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Laboratoire de Biologie et Génétique du Cancer, Centre François Baclesse | - | - - |
Benign, no assertion criteria provided | clinical testing | Sharing Clinical Reports Project (SCRP) | Sep 16, 2011 | - - |
Benign, no assertion criteria provided | clinical testing | Department of Medical and Surgical Sciences, University of Bologna | Sep 01, 2023 | 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) - |
Benign, no assertion criteria provided | clinical testing | BRCAlab, Lund University | Mar 02, 2020 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Michigan Medical Genetics Laboratories, University of Michigan | Nov 03, 2014 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | 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. - |
Likely benign, criteria provided, single submitter | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | May 31, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | Oct 09, 2014 | - - |
not provided Uncertain:4Benign:4
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Sep 05, 2017 | 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. - |
Uncertain significance, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | 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. - |
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 09, 2021 | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute | - | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Aug 17, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Jul 26, 2023 | - - |
Hereditary breast ovarian cancer syndrome Uncertain:2Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Likely benign, criteria provided, single submitter | research | Genetics Program, Instituto Nacional de Cancer | Nov 01, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | National Health Laboratory Service, Universitas Academic Hospital and University of the Free State | Apr 19, 2022 | - - |
Uncertain significance, no assertion criteria provided | research | Hereditary Cancer Genetics group, Vall d'Hebron Institute of Oncology | Mar 01, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Mendelics | Aug 22, 2023 | - - |
not specified Benign:4
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Dec 12, 2022 | 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. - |
Benign, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital | Aug 15, 2023 | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Hereditary cancer-predisposing syndrome Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 08, 2019 | 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. - |
Likely benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | May 10, 2022 | - - |
Breast and/or ovarian cancer Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research | Aug 23, 2013 | - - |
Medulloblastoma;C0346153:Familial cancer of breast;C0376358:Malignant tumor of prostate;C1838457:Fanconi anemia complementation group D1;C2675520:Breast-ovarian cancer, familial, susceptibility to, 2;C2751641:Glioma susceptibility 3;C3150546:Pancreatic cancer, susceptibility to, 2;CN033288:Wilms tumor 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Mar 30, 2022 | - - |
BRCA2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 13, 2022 | 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). - |
Computational scores
Source:
Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at