ClinVar Genomic variation as it relates to human health

The c.831T>G variant in BRCA2 is a missense variant predicted to cause substitution of Asparagine by Lysine at amino acid 277 (p.Asn277Lys). The highest non-cancer, non-founder population filter allele frequency in gnomAD v2.1 (exomes only, non-cancer subset, read depth >=20) or gnomAD v3.1 (non-cancer subset, read depth >=20) is 0.00008331 in the European (non-Finnish) population, which is within the ENIGMA BRCA1/2 VCEP threshold (>0.00002 to <= 0.0001) for BS1_Supporting (BS1_Supporting met). This missense variant is located outside of a key functional domain and was not predicted to alter mRNA splicing using the SpliceAI predictor (score 0, score threshold <0.1) (BP1_Strong met). Reported by one calibrated study to exhibit protein function similar to benign control variants (PMID: 33293522) (BS3 met). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 0.06 (based on Cosegregation LR=0.3; Pathology LR=1.27; Co-occurrence LR=1.88; Family History LR=0.0888), within the thresholds for Moderate benign evidence (LR >=0.05 & <0.23) (BP5_Moderate met; PMID: 31131967). In summary, this variant meets the criteria to be classified as a Benign variant for BRCA2-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (BS1_Supporting, BP1_Strong, BS3, BP5_Moderate).

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: 1 report identified this varint in a prostate cancer cohort - reported as unclassified variant; ClinVar: 3 VUS, 2 LB/B

Variant summary: BRCA2 c.831T>G (p.Asn277Lys) 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 7.3e-05 in 245138 control chromosomes, exclusively within the Non-Finnish European subpopulation at a frequency of 0.00016 in the gnomAD database. This frequency is not higher than expected for a pathogenic variant in BRCA2 causing Hereditary Breast And Ovarian Cancer Syndrome (7.3e-05 vs 0.00075), allowing no conclusion about variant significance. c.831T>G has been reported in the literature in individuals affected with breast, ovarian, and other cancers, however these reports do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. Multiple co-occurrences with other pathogenic variants have been reported (UMD: BRCA2 c.5909C>A, p.Ser1970X; BIC: BRCA1 c.2685_2686delAA, p.Pro897Lysfs; internal sample from a male patient: BRCA2 c.5386_5387delGA, p.Asp1796fsX10), providing supporting evidence for a benign role. Moreover, a recent report from the CAGI5 (fifth Critical Assessment of Genome Interpretation) challenge has classified this variant as benign in a prediction protocol that includes assessment of the impact of this variant on splicing and protein function using four sets of predictors (Padilla_2019). An experimental study determined the variant to be 'functional' based on cell survival and drug sensitivity assay results (Biswas_2020). Multiple submitters have provided assessments for this variant to ClinVar after 2014 with conflicting assessments (likely benign n=6, VUS n=6, likely pathogenic n=1). Based on the evidence outlined above, the variant was classified as likely benign.

This variant is associated with the following publications: (PMID: 16683254, 21952622, 28435519, 31432501, 22771033, 18724707, 10923033, 21533266, 27153395, 24817641, 25348012, 22476429, 31131967)

The frequency of this variant in the general population, 0.00015 (19/127296 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported in individuals with early-onset prostate cancer (PMID: 21952622 (2011)), pancreatic cancer (PMIDs: 31432501 (2019) and 34597585 (2021)), and breast and/or ovarian cancer (PMIDs: 26543556 (2015), 27153395 (2016), 28435519 (2017), 30086788 (2018), 31131967 (2019), and 32438681 (2020)). In a large breast cancer association study, the variant was reported in both individuals with breast cancer and healthy individuals (PMID: 33471991 (2021), see also LOVD (https://databases.lovd.nl/shared/variants/BRCA2)). Functional studies suggest conflicting reports of the variant's impact on protein function (PMIDs: 22771033 (2012) and 33293522 (2020)). 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.

The BRCA2 c.831T>G; p.Asn277Lys variant (rs28897705) is reported in the literature in individuals affected with breast, ovarian, prostate, or pancreatic cancer, although it was not demonstrated to be disease-causing (Kote-Jarai 2011, Schubert 2017, Schwartz 2019, van der Hout 2006). This variant is found in the non-Finnish European population with an overall allele frequency of 0.01% (19/127296 alleles) in the Genome Aggregation Database. The asparagine at codon 277 is moderately conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Consistent with predictions, one study observed the p.Asn277Lys variant disrupted interactions with factors involved with cytokinesis, and its expression in cultured cells correlated with a higher percentage of multinucleate cells (Mondal 2012), although the clinical significance of these observations has not been demonstrated. Due to limited information, the clinical significance of the p.Asn277Lys variant is uncertain at this time. References: Kote-Jarai Z et al. BRCA2 is a moderate penetrance gene contributing to young-onset prostate cancer: implications for genetic testing in prostate cancer patients. Br J Cancer. 2011;105(8):1230-1234. Mondal G et al. BRCA2 localization to the midbody by filamin A regulates cep55 signaling and completion of cytokinesis. Dev Cell. 2012;23(1):137-152. Schubert S et al. GT198 (PSMC3IP) germline variants in early-onset breast cancer patients from hereditary breast and ovarian cancer families. Genes Cancer. 2017;8(1-2):472-483. Schwartz M et al. Familial pancreatic adenocarcinoma: A retrospective analysis of germline genetic testing in a French multicentre cohort. Clin Genet. 2019;96(6):579-584. van der Hout AH et al. A DGGE system for comprehensive mutation screening of BRCA1 and BRCA2: application in a Dutch cancer clinic setting. Hum Mutat. 2006;27(7):654-666.

Missense variant in a coldspot region where missense variants are very unlikely to be pathogenic (PMID:31911673).

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.

BRCA2: BP4

The BRCA2 p.Asn277Lys variant was identified in 1 of 8048 proband chromosomes (frequency: 0.0001) from individuals or families with breast and ovarian cancer (van der Hout 2006). The variant was also identified in the following databases: dbSNP (ID: rs28897705) as With other allele, ClinVar (conflicting interpretations of pathogenicity), Clinvitae (conflicting interpretations of pathogenicity), COGR (uncertain significance), MutDB, LOVD 3.0 (26X), UMD-LSDB (16X likely neutral), BIC Database (12X unknown significance). The variant was not identified in Cosmic, ARUP Laboratories, or Zhejiang Colon Cancer Databases. In UMD the variant was identified with a co-occurring pathogenic BRCA2 variant (c.5909C>A (p.Ser1970X)), increasing the likelihood that the p.Asn277Lys variant does not have clinical significance. In addition, the variant was identified with a co-occurring pathogenic BRCA2 variant (c.4042delT (p.Cys1348ValfsX26)) in on individual from our laboratory, increasing the likelihood that the p.Asn277Lys variant does not have clinical significance. The variant was identified in control databases in 18 of 271412 chromosomes at a frequency of 0.000066 increasing the likelihood that this may be a low frequency variant in certain populations of origin (Genome Aggregation Consortium Feb 27, 2017). The functional study by Mondal (2012) suggested that the variant protein disrupted protein interactions, resulting in cytokinetic defects, but had no effect on BRCA2-dependent homologous recombination. The p.Asn277 residue is conserved in mammals but not in more distantly related organisms however four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and 2 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.