ClinVar Genomic variation as it relates to human health

This variant is considered likely benign or benign based on one or more of the following: it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease, and/or has normal protein function, and/or has lack of segregation with disease, and/or has been detected in co-occurrence with known pathogenic variant, and/or has lack of disease association in case-control studies, and/or is located in a region inconsistent with a known cause of pathogenicity.

DNA sequence analysis of the BRCA2 gene demonstrated a sequence change, c.280C>T, in exon 3 that results in an amino acid change, p.Pro94Ser. This sequence change does not appear to have been previously described in patients with BRCA2-related disorders and has been described in the gnomAD database with a frequency of 0.014% in the Latino sub-population (dbSNP rs80358531). The p.Pro94Ser change affects a moderately conserved amino acid residue located in a domain of the BRCA2 protein that is known to be functional. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL) provide contradictory results for the p.Pro94Ser substitution. Due to these contrasting evidences and the lack of functional studies, the clinical significance of the p.Pro94Ser change remains unknown at this time.

In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 21120943, 19471317, 25348012, 29659569, 29928469, 32641407, 32123317)

Variant summary: BRCA2 c.280C>T (p.Pro94Ser) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4.8e-05 in 251082 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in BRCA2 causing Hereditary Breast And Ovarian Cancer Syndrome (4.8e-05 vs 0.00075), allowing no conclusion about variant significance. c.280C>T has been reported in the literature in individuals affected with breast or ovarian cancer and HBOC (example, Caux-Moncoutier_2009, Ortiz_2016, Maksimenko_2018, Guindalini_2022). These report(s) do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. At-least one co-occurrence with another pathogenic variant has been observed (BRCA1 c.5266dup, p.Gln1756fsX74 in UMD database), providing supporting evidence for a benign role. This variant had no effect in a study assessing allelic imbalance as an indirect measure of the impact of out-of-frame defects leading to reductions in the levels of mutant mRNA cleared through NMD (example, Caux-Moncoutier 2009). Consistent with this result, a second study has shown variant has no effect on splicing and classified the variant as benign (Thomassen_ 2022). This supports the notion that this variant has no effect on splicing. The following publications have been ascertained in the context of this evaluation (PMID: 19471317, 21120943, 29928469, 29659569, 35979650, 35264596). Eleven submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as likely benign (n=4) and VUS (n=7). Based on the evidence outlined above, the variant was classified as likely benign.

In the published literature, the variant has been reported individuals with hereditary breast and ovarian cancer (PMID: 29928469 (2018) and 21120943 (2011)). Published studies indicate that this variant does not alter splicing (PMID: 32641407 (2020), 32123317 (2020)) and does not demonstrate allelic imbalance (PMID: 19471317 (2009)). The frequency of this variant in the general population, 0.00014 (5/34570 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded conflicting predictions that this variant is benign or damaging. Based on the available information, we are unable to determine the clinical significance of this variant.

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.

The p.Pro94Ser variant was identified by Caux-Moncoutier (2009) in a hereditary breast/ovarian cancer (HBOC) patient. The authors of this study used an allelic imbalance assay to assess the putative impact of variants on splicing; no allelic imbalance was found for the variant, suggesting that it does not impact splicing. The variant was also identified in dbSNP (ID: rs80358531) “With non-pathogenic allele”, and three times in UMD as an unclassified variant. The p.Pro94 residue is conserved across mammals and lower organisms and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM) suggest that the p.Pro94Ser variant may impact the protein. However, this information is not predictive enough to assume pathogenicity. 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.

BS1(Supporting)+BP1(Strong)+BP5(Moderate) 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)

The BRCA2 c.280C>T variant is predicted to result in the amino acid substitution p.Pro94Ser. This variant was reported as uncertain significance in individuals with a personal or family history of hereditary breast and/or ovarian cancer (Table 1b, Caux-Moncoutier et al. 2009. PubMed ID: 19471317; Table S2B, Caux-Moncoutier et al. 2011. PubMed ID: 21120943; Patient 8 in Tables 2 and 3, Maksimenko et al. 2018. PubMed ID: 29928469). This variant was also documented in a prostate cancer cohort (Table S2, Paulo et al. 2018. PubMed ID: 29659569). Blood RNA analysis showed that this variant does not affect normal splicing (Table S1, Wai et al. 2020. PubMed ID: 32123317). This variant is reported in 0.014% of alleles in individuals of Latino descent in gnomAD and has conflicting interpretations of pathogenicity in ClinVar ranging from benign to uncertain (http://www.ncbi.nlm.nih.gov/clinvar/variation/37803). Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.