13-32329440-C-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PP4_ModeratePVS1_ModeratePM3
This summary comes from the ClinGen Evidence Repository: The c.632-3C>G variant is an intronic variant occurring in intron 7 of the BRCA2 gene. This variant is present in gnomAD v2.1 (exomes only, non-cancer subset) or gnomAD v3.1 (non-cancer subset) but is below the ENIGMA BRCA1/2 VCEP threshold >0.00002 for BS1_Supporting (PM2_Supporting, BS1, and BA1 are not met). This variant is reported to result in aberrant mRNA splicing. RT-PCR and Mini-gene assays demonstrated that the variant impacts splicing by creating a new acceptor splice site, resulting in retention of 2bp from intron 7, which leads to a frameshift and generates a premature stop codon (PMIDs: 30883759, 32123317, 22505045). Reduced expression of aberrant transcript reported by one assay suggesting potential incomplete expression of the aberrant transcript (Ambry internal contributor). Appropriate code strength determined by comparison of results to PVS1 decision tree PVS1 (RNA) was downgraded to PVS1_Moderate (RNA). This variant has been detected in 2 siblings with phenotype consistent with BRCA2-Fanconi Anemia (FA). At least two clinical features of FA (physical features, pathology findings and cancer diagnosis ≤5yr) and confirmed chromosome breakage, are seen in these individuals. Both siblings were homozygous for the variant. Total points equated to 2 (PM3 met; PMID:25381700). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 12.477 (based on Pathology LR=1.07; Co-occurrence LR=1.0498; Family History LR=11.107), within the thresholds for Moderate evidence towards pathogenicity (LR >4.3 & ≤18.7) (PP4_Moderate met; PMID:31131967, 31853058). In summary, this variant meets the criteria to be classified as a Likely pathogenic variant for BRCA2-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (PVS1_Moderate (RNA), PM3, PP4_Moderate). LINK:https://erepo.genome.network/evrepo/ui/classification/CA348611/MONDO:0012933/097
Frequency
Consequence
NM_000059.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BRCA2 | ENST00000380152.8 | c.632-3C>G | splice_region_variant, intron_variant | Intron 7 of 26 | 5 | NM_000059.4 | ENSP00000369497.3 | |||
BRCA2 | ENST00000530893.7 | c.263-3C>G | splice_region_variant, intron_variant | Intron 7 of 26 | 1 | ENSP00000499438.2 | ||||
BRCA2 | ENST00000614259.2 | n.632-3C>G | splice_region_variant, intron_variant | Intron 6 of 25 | 2 | ENSP00000506251.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000411 AC: 1AN: 243142Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 131370
GnomAD4 exome AF: 0.00000139 AC: 2AN: 1438228Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 716226
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74450
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Pathogenic:2Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2023 | The c.632-3C>G intronic variant results from a C to G substitution 3 nucleotides upstream from coding exon 7 in the BRCA2 gene. 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 and will result in the creation or strengthening of a novel splice acceptor site. This alteration results in use of this novel cryptic acceptor site two nucleotides upstream of the native site resulting in a frameshifting transcript (Ambry internal data; Houdayer C et al. Hum. Mutat. 2012 Aug;33(8):1228-38; Fraile-Bethencourt E et al. J. Pathol., 2019 08;248:409-420). In addition, this alteration has been shown to express an in-frame transcript, known as 6q39_8 in the literature (Ambry internal data). This transcript has been shown to be able to perform homology directed repair in protein functional studies at a near wild-type level (Mesman, RLS et al. Genet Med 2020 08;22(8):1355-1365). This alteration was identified as homozygous in a fetus with features consistent with Fanconi anemia (Malric, A et al. Pediatr Blood Cancer 2015 Mar;62(3):463-70). Since supporting evidence is conflicting at this time, the clinical significance of this alteration remains unclear. - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | May 19, 2020 | This variant causes a C to G nucleotide substitution at the -3 position of intron 7 of the BRCA2 gene. Splice site prediction tools suggest that this variant may have a significant impact on RNA splicing. Functional RNA studies have shown that this variant causes the use of an alternative splice acceptor site 2-nucleotide upstream of the reference acceptor site, creating premature translation stop signal in the RNA transcripts (PMID: 22505045, 30883759). The aberrant transcripts are expected to result in an absent or non-functional protein product. This variant has been reported in individuals affected with breast and/or ovarian cancer (PMID: 22505045, Color internal data). In addition, a multifactorial likelihood model using health history and tumor pathology data has suggested this variant have a high probability of being pathogenic (PMID: 31131967). This variant has been identified in 1/243142 chromosomes 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 Likely Pathogenic. - |
Likely pathogenic, criteria provided, single submitter | curation | Sema4, Sema4 | Sep 11, 2021 | - - |
not provided Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Jul 28, 2023 | Non-canonical splice site variant demonstrated to result in loss-of-function (Houdayer et al., 2012; Fraile-Bethencourt et al., 2019); Multifactorial likelihood analysis suggests this variant is pathogenic (Parsons et al., 2019); Not observed at significant frequency in large population cohorts (gnomAD); Also known as 860-3C>G; This variant is associated with the following publications: (PMID: 26913838, 22505045, 29750258, 25416802, 32123317, 33466630, 30883759, 33646313, 25381700, 31131967) - |
Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | BRCA2: PVS1, PM2, PS3:Supporting - |
Hereditary breast ovarian cancer syndrome Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 11, 2024 | This sequence change falls in intron 7 of the BRCA2 gene. It does not directly change the encoded amino acid sequence of the BRCA2 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or altered protein product. This variant is present in population databases (rs568027879, gnomAD 0.007%). This variant has been observed in individual(s) with a personal and/or family history of breast and/or ovarian cancer (PMID: 22505045, 33466630, 33646313). ClinVar contains an entry for this variant (Variation ID: 219896). Based on a multifactorial likelihood algorithm using genetic, in silico, and/or statistical data, this variant has been determined to have a high probability of being pathogenic (PMID: 31131967). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in introduction of a cryptic splice acceptor site, and produces a non-functional protein and/or introduces a premature termination codon (PMID: 22505045, 30883759, 32123317; internal data). For these reasons, this variant has been classified as Pathogenic. - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Feb 17, 2025 | Variant summary: BRCA2 c.632-3C>G, also reported as IVS07-3C>G(c.630dupAG) (intron7), alters a non-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 creates a 3' acceptor site. Three predict the variant abolishes a 3' acceptor site. One predicts the variant weakens a 3' acceptor site. At least one publication reports experimental evidence that this variant affects mRNA splicing. In vitro minigene assays determined there are 2 predicted impacts on RNA splicing; the first inserts 2 nucleotides immediately upstream of exon 8 (r.631_632ins632-1_632-2), resulting in p.Val211Glufs*18, and the second results in the skipping of exons 6_7 and insertion of 2 nucleotides upstream of exon 8 (r.478_631delins632-1_632-2), resulting in p.Gly173Lysfs*2. The aberrant transcripts comprised approximately 75% and 25% of the minigene transcript pool, respectively (example, Fraile-Bethencourt_2019) and no remaining wild type transcript was reported. In vivo RNA analysis (internal, Labcorp Genetics (formerly Invitae)) corroborated the r.631_632ins632-2_632-1 impact, which is predicted to result in nonsense mediated decay. The variant allele was found at a frequency of 4.1e-06 in 243142 control chromosomes. c.632-3C>G has been reported in the homozygous or presumed compound heterozygous state in the literature in at least 2 individuals affected with autosomal recessive Fanconi anemia (example, Malric_2015, Radulovic_2023). Further, it has also been reported in the heterozygous state in individual(s) with clinical features of Hereditary Breast and Ovarian Cancer (example, George_2021, Vasconcelos_2021). These data indicate that the variant may be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 30883759, 33646313, 22505045, 25381700, 36721989, 33466630, 32123317). ClinVar contains an entry for this variant (Variation ID: 219896). Based on the evidence outlined above, the variant was classified as likely pathogenic. - |
Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:1
Likely pathogenic, no assertion criteria provided | clinical testing | Sharing Clinical Reports Project (SCRP) | Dec 06, 2011 | - - |
BRCA2-related cancer predisposition Pathogenic:1
Likely pathogenic, reviewed by expert panel | curation | ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen | Jun 11, 2024 | The c.632-3C>G variant is an intronic variant occurring in intron 7 of the BRCA2 gene. This variant is present in gnomAD v2.1 (exomes only, non-cancer subset) or gnomAD v3.1 (non-cancer subset) but is below the ENIGMA BRCA1/2 VCEP threshold >0.00002 for BS1_Supporting (PM2_Supporting, BS1, and BA1 are not met). This variant is reported to result in aberrant mRNA splicing. RT-PCR and Mini-gene assays demonstrated that the variant impacts splicing by creating a new acceptor splice site, resulting in retention of 2bp from intron 7, which leads to a frameshift and generates a premature stop codon (PMIDs: 30883759, 32123317, 22505045). Reduced expression of aberrant transcript reported by one assay suggesting potential incomplete expression of the aberrant transcript (Ambry internal contributor). Appropriate code strength determined by comparison of results to PVS1 decision tree PVS1 (RNA) was downgraded to PVS1_Moderate (RNA). This variant has been detected in 2 siblings with phenotype consistent with BRCA2-Fanconi Anemia (FA). At least two clinical features of FA (physical features, pathology findings and cancer diagnosis <=5yr) and confirmed chromosome breakage, are seen in these individuals. Both siblings were homozygous for the variant. Total points equated to 2 (PM3 met; PMID: 25381700). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 12.477 (based on Pathology LR=1.07; Co-occurrence LR=1.0498; Family History LR=11.107), within the thresholds for Moderate evidence towards pathogenicity (LR >4.3 & <=18.7) (PP4_Moderate met; PMID: 31131967, 31853058). In summary, this variant meets the criteria to be classified as a Likely pathogenic variant for BRCA2-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (PVS1_Moderate (RNA), PM3, PP4_Moderate). - |
Familial cancer of breast Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Oct 10, 2022 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Feb 28, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at