chr13-32326497-A-G
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Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1_ModeratePP5_Very_Strong
The NM_000059.4(BRCA2):c.517-2A>G variant causes a splice acceptor change. The variant allele was found at a frequency of 0.00000968 in 1,446,636 control chromosomes in the GnomAD database, with no homozygous occurrence. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000097 ( 0 hom. )
Consequence
BRCA2
NM_000059.4 splice_acceptor
NM_000059.4 splice_acceptor
Scores
3
1
3
Splicing: ADA: 1.000
2
Clinical Significance
Conservation
PhyloP100: 5.86
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 Pathogenic. Variant got 10 ACMG points.
PVS1
Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.011114361 fraction of the gene. Cryptic splice site detected, with MaxEntScore 3.7, offset of 9, new splice context is: tttcctcccggggtcgtcAGaca. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.
PP5
Variant 13-32326497-A-G is Pathogenic according to our data. Variant chr13-32326497-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 51801.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32326497-A-G is described in Lovd as [Pathogenic]. Variant chr13-32326497-A-G is described in Lovd as [Pathogenic].
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| BRCA2 | NM_000059.4 | c.517-2A>G | splice_acceptor_variant | ENST00000380152.8 | NP_000050.3 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| BRCA2 | ENST00000380152.8 | c.517-2A>G | splice_acceptor_variant | 5 | NM_000059.4 | ENSP00000369497 | A2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000968 AC: 14AN: 1446636Hom.: 0 Cov.: 30 AF XY: 0.0000139 AC XY: 10AN XY: 720642
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14
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1446636
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30
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10
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720642
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GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:22
Revision: reviewed by expert panel
LINK: link
Submissions by phenotype
Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:8
| 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 = 0.999418 - |
| Pathogenic, criteria provided, single submitter | clinical testing | Counsyl | May 01, 2017 | - - |
| 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, no assertion criteria provided | clinical testing | BRCAlab, Lund University | Aug 26, 2022 | - - |
| Likely pathogenic, no assertion criteria provided | clinical testing | Sharing Clinical Reports Project (SCRP) | Jan 06, 2011 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Oct 22, 2020 | The BRCA2 c.517-2A>G variant results in a substitution at the consensus splice acceptor site which is has been shown to result in a skipping of exon 7, resulting in a frameshift and premature stop codon (Houdayer et al. 2012; Casadei et al. 2019). This variant has been identified in individuals with hereditary breast and ovarian cancer and in at least one male with metastatic prostate cancer (Jakubowska et al. 2003; Song et al. 2014; Pritchard et al. 2016; Heramb et al. 2018; Casadei et al. 2019) and also in individuals with a phenotype consistent with Fanconi anemia (Maramatsu et al. 2017; Mori et al. 2019). This variant is not observed in version 2.1.1 of the Genome Aggregation Database. Based on the collective evidence the c.517-2A>G variant is classified as pathogenic for hereditary breast and ovarian cancer. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Department of Medical Genetics, Oslo University Hospital | Jan 20, 2017 | - - |
Hereditary breast ovarian cancer syndrome Pathogenic:5
| Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Nov 13, 2019 | Variant summary: BRCA2 c.517-2A>G 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: Five predict the variant abolishes a 3 acceptor site. Experimental evidence are in support of these predictions and demonstrated exon 7 skipping following in vitro analysis (Houdayer_2012). The variant was absent in 251306 control chromosomes (gnomAD). c.517-2A>G has been reported in the literature in multiple individuals affected with Hereditary Breast and Ovarian Cancer and also prostate cancer (e.g. Jakubowska_2003, Pritchard_2016, Rebbeck_2018, Song_2014, Walsh_2011). These data indicate that the variant is very likely to be associated with disease. Nine ClinVar submitters (evaluation after 2014) cite the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | This sequence change affects an acceptor splice site in intron 6 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 breast cancer, ovarian cancer and Fanconi anemia (PMID: 14647210, 24728189, 26681682, 27836010, 28102861). ClinVar contains an entry for this variant (Variation ID: 51801). Studies have shown that disruption of this splice site alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 22505045, 30883759; Invitae). For these reasons, this variant has been classified as Pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | - - |
| 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 | Dec 23, 2016 | The c.517-2A>G variant in BRCA2 has been reported in at least 6 individuals with BRCA2-associated cancers (Jakubowska 2003, Breast Cancer Information Core (BIC) database) and was absent from large population studies. In vitro functional stu dies provide some evidence that the c.517-2A>G variant may impact protein functi on (Houdayer 2012). This variant occurs in the invariant region (+/- 1,2) of the splice consensus sequence and is predicted to cause altered splicing leading to an abnormal or absent protein. Heterozygous loss of function of the BRCA2 gene is an established disease mechanism in hereditary breast and ovarian cancer (HBO C). In summary, this variant meets criteria to be classified as pathogenic for H BOC in an autosomal dominant manner. - |
not provided Pathogenic:3
| Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | May 29, 2024 | Canonical splice site variant demonstrated to result in multiple isoforms, including out-of-frame skipping of exon 7 as well as in-frame skipping of exons 4-7, that could result in a hypomorphic allele associated with lower cancer risks than those of typical BRCA2 pathogenic variants (PMID: 22505045, 30883759, 32398771); Observed with a BRCA2 truncating variant in a patient with features consistent with Fanconi anemia, as well as homozygous in a patient with atypical Fanconi anemia presentation (PMID: 28102861, 30792206, Mike Leach FRCP et al. (2015) Practical Flow Cytometry in Haematology Diagnosis: 100 Worked Examples.); Observed in individuals with breast, ovarian, or prostate cancer (PMID: 14647210, 24728189, 26681682, 27208206, 27433846, 31263054, 32427313); Published functional studies demonstrate intermediate homology-directed repair activity, intermediate null cell complementation, and reduced protein level (PMID: 32398771); Not observed at significant frequency in large population cohorts (gnomAD); Multifactorial likelihood analysis suggests this variant is pathogenic (PMID: 31131967); Also known as 745-2A>G; This variant is associated with the following publications: (PMID: 14647210, 36551643, 36721989, 24728189, 25525159, 27433846, 27836010, 26681682, 21523855, 27208206, 28152038, 30787465, 28102861, 33654310, 29852322, 29339979, 22505045, 34413315, 32427313, 29176636, 29446198, 31263054, 31853058, 30792206, 31131967, 33471991, 30652428, 30883759, 31843900, 32398771) - |
| Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Sep 24, 2022 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Jun 22, 2023 | The BRCA2 c.517-2A>G variant disrupts a canonical splice-acceptor site and interferes with normal BRCA2 mRNA splicing. This variant has been reported in the published literature in individuals with breast cancer (PMID: 32427313 (2020), 30652428 (2019), 27836010 (2016), 26681682 (2016)) and ovarian cancer (PMID: 14647210 (2003)). This variant was also reported to result in aberrant splicing and skipping of BRCA2 exon 7 (PMID: 30883759 (2019), 22505045 (2012)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Based on the available information, this variant is classified as pathogenic. - |
Hereditary cancer-predisposing syndrome Pathogenic:2
| Pathogenic, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Mar 30, 2023 | This variant causes an A to G nucleotide substitution at the -2 position of intron 6 of the BRCA2 gene. This variant is also known as IVS6-2A>G and 745-2A>G in the literature. RNA studies have detected the out-of-frame skipping of exon 7 in carrier-derived RNA and in minigene splicing assays (PMID: 22505045, 30883759, 31843900). This variant has been reported in at least six individuals affected with breast and/or ovarian cancer (PMID: 14647210, 24240112, 24728189, 26681682, 33471991; Leiden Open Variation Database DB-ID BRCA2_003448) and in additional suspected hereditary breast and ovarian cancer families (PMID: 29176636, 29339979, 29446198). This variant also has been detected in an individual affected with prostate cancer (PMID: 27433846). The variant has been reported with segregation, tumor pathology and family history likelihood ratios for pathogenicity of 3.4966, 3.8211 and 3.1152, respectively (PMID: 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 (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 11, 2023 | The c.517-2A>G intronic variant results from an A to G substitution 2 nucleotides upstream from coding exon 6 in the BRCA2 gene. This alteration has been identified in the homozygous state and with another truncating BRCA2 variant (phase unknown) in patients with Fanconi Anemia (Leach M et al. Practical Flow Cytometry in Hematology: 100 worked examples. 321-324; 2015; Muramatsu H et al. Genet. Med., 2017 07;19:796-802). This alteration has also been reported in the heterozygous state in individuals diagnosed with ovarian, breast and aggressive prostate cancer (Jakubowska A et al. Eur J Hum Genet. 2003 Dec;11(12):955-8; Eccles DM et al. Ann. Oncol., 2016 Mar;27:467-73; Song H et al. Hum. Mol. Genet., 2014 Sep;23:4703-9; Rebbeck TR et al. Breast Cancer Res., 2016 11;18:112; Pritchard CC et al. N. Engl. J. Med., 2016 Aug;375:443-53; Palmer JR et al. J Natl Cancer Inst, 2020 12;112:1213-1221). This alteration has been classified as pathogenic by multifactorial analysis, which integrates the following lines of evidence to produce a quantitative likelihood of pathogenicity: in silico prediction models, segregation with disease, tumor characteristics, and mutation co-occurrence (Parsons MT et al. Hum. Mutat. 2019 09;40(9):1557-1578). Of note, this alteration is also designated as IVS6-2A>G in published literature. This nucleotide position is well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site. This alteration results in skipping of coding exon 6 in multiple different RNA studies (Ambry internal data; Houdayer C et al. Hum Mut. 2012; 33:1228–38; Fraile-Bethencourt E et al. J. Pathol. 2019 08;248(4):409-420). This alteration partially complemented survival in a Brca2-null mouse embryonic stem cell assay and surviving cells retained partial homology-directed DNA repair activity which could be imparted by the weak expression of an in-frame rescue transcript (Mesman RLS et al. Genet Med, 2020 08;22:1355-1365). Based on the majority of available evidence to date, this variant is likely to be pathogenic. However, because this variant is identified in one or more patients with Fanconi Anemia it may be hypomorphic and thus, carriers of this variant and their families may present with reduced risks, and not with the typical clinical characteristics of a high-risk pathogenic BRCA2 alteration. As risk estimates are unknown at this time, clinical correlation is advised. - |
Hereditary breast ovarian cancer syndrome;C2675520:Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:1
| Pathogenic, no assertion criteria provided | research | King Laboratory, University of Washington | Sep 01, 2019 | - - |
BRCA2-related cancer predisposition Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Sep 27, 2024 | This variant causes an A to G nucleotide substitution at the -2 position of intron 6 of the BRCA2 gene. This variant is also known as IVS6-2A>G and 745-2A>G in the literature. RNA studies have detected the out-of-frame skipping of exon 7 in carrier-derived RNA and in minigene splicing assays (PMID: 22505045, 30883759, 31843900). This variant has been reported in at least six individuals affected with breast and/or ovarian cancer (PMID: 14647210, 24240112, 24728189, 26681682, 33471991; Leiden Open Variation Database DB-ID BRCA2_003448) and in additional suspected hereditary breast and ovarian cancer families (PMID: 29176636, 29339979, 29446198). This variant also has been detected in an individual affected with prostate cancer (PMID: 27433846). The variant has been reported with segregation, tumor pathology and family history likelihood ratios for pathogenicity of 3.4966, 3.8211 and 3.1152, respectively (PMID: 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 (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. - |
BRCA2-related disorder Pathogenic:1
| Pathogenic, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 06, 2024 | The BRCA2 c.517-2A>G variant is predicted to disrupt the AG splice acceptor site and interfere with normal splicing. This variant was reported in individuals with breast and/or ovarian cancer (Jakubowska et al 2003. PubMed ID: 14647210; Pennington KP et al 2013. PubMed ID: 24240112; Song H et al 2014. PubMed ID: 24728189; Eccles DM et al 2015. PubMed ID: 26681682; Breast Cancer Association Consortium et al 2021. PubMed ID: 33471991). This variant was also reported in an individual with prostate cancer (Pritchard CC et al 2016. PubMed ID: 27433846). RNA studies of this variant have demonstrated disrupted splicing (Houdayer C et al 2012. PubMed ID: 22505045). This variant has not been reported in a large population database, indicating this variant is rare. This variant is interpreted as pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/51801/). Variants that disrupt the consensus splice acceptor site in BRCA2 are expected to be pathogenic. This variant is interpreted as pathogenic. - |
Familial cancer of breast Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Feb 01, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Benign
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
MutationTaster
Benign
D;D
GERP RS
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AL_spliceai
Position offset: 2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at