13-32326497-A-G
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, intron 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
Consequence
NM_000059.4 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| BRCA2 | ENST00000380152.8 | c.517-2A>G | splice_acceptor_variant, intron_variant | Intron 6 of 26 | 5 | NM_000059.4 | ENSP00000369497.3 | |||
| BRCA2 | ENST00000530893.7 | c.148-2A>G | splice_acceptor_variant, intron_variant | Intron 6 of 26 | 1 | ENSP00000499438.2 | ||||
| BRCA2 | ENST00000614259.2 | n.517-2A>G | splice_acceptor_variant, intron_variant | Intron 5 of 25 | 2 | ENSP00000506251.1 |
Frequencies
GnomAD3 genomes
GnomAD4 exome AF: 0.00000968 AC: 14AN: 1446636Hom.: 0 Cov.: 30 AF XY: 0.0000139 AC XY: 10AN XY: 720642
GnomAD4 genome
ClinVar
Submissions by phenotype
Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:8
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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. -
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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 -
Hereditary breast ovarian cancer syndrome Pathogenic:5
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. -
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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. -
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 altered 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. -
not provided Pathogenic:3
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) -
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. -
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Hereditary cancer-predisposing syndrome Pathogenic:2
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. -
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. -
Hereditary breast ovarian cancer syndrome;C2675520:Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:1
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BRCA2-related cancer predisposition Pathogenic:1
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
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
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at