ClinVar Genomic variation as it relates to human health

The frequency of this variant in the general population, 0.0002 (4/19940 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, this variant has been reported in individuals affected with breast cancer (PMIDs: 36329109 (2022), 33471991 (2021) and 21218378 (2010)), as well as in individuals at high-risk for hereditary breast and/or ovarian cancer (PMID: 31742824 (2020)). It has also been observed in healthy control individuals (PMIDs: 33471991 (2021); LOVD3 Shared (https://databases.lovd.nl/shared/) and 32467295 (2020)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is benign. Based on the available information, we are unable to determine the clinical significance of this variant.

This variant is associated with the following publications: (PMID: 21218378)

The BRCA2 c.9728C>T variant is predicted to result in the amino acid substitution p.Pro3243Leu. This variant was reported in a breast cancer patient with Korean-Hawaiian ancestry (see patient #45 in Table 1, Carney et al. 2010. PubMed ID: 21218378), however the patient had a family member with breast cancer who was positive for a different uncertain BRCA2 variant and it is unclear if the p.Pro3243Leu variant was a cause of disease. This variant was also reported in two Chinese breast cancer cohort studies (Supplementary Table S2, Shao et al. 2019. PubMed ID: 31742824; Supplementary Table 1, Dong et al. 2021. PubMed ID: 32467295). Computational functional effect prediction programs classified this variant as probably benign (Pejaver et al. 2017. PubMed ID: 28508593). This variant is reported in 0.020% of alleles in individuals of East Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/13-32972378-C-T) and has conflicting interpretations regarding its pathogenicity in ClinVar, ranging from likely benign to uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/38262/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

Variant summary: BRCA2 c.9728C>T (p.Pro3243Leu) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. Consensus agreement among computation tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 1.2e-05 in 251118 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.9728C>T has been reported in the literature as a VUS in settings of individuals affected with and/or undergoing multigene panel testing for Hereditary Breast And Ovarian Cancer (e.g., Carney_2010, Shao_2020) as well as in at least one individual diagnosed with triple-negative breast cancer (e.g., Matta_2022), however without strong evidence for causality in these instances (e.g., lack of co-segregation data). These reports therefore do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 21218378, 32467295, 36329109, 28508593, 31742824). ClinVar contains an entry for this variant (Variation ID: 38262). Based on an emerging peer consensus and the lack of any evidence supporting an actionable outcome as outlined above, the variant was re-classified as likely benign.

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.Pro3243Leu variant was not identified in the literature, nor was it identified in NHLBI Exome Sequencing Project (Exome Variant Server), HGMD, LOVD, COSMIC, GeneInsight VariantWire, BIC or UMD. The variant was identified in the dbSNP database (ID#:rs80359241), but no frequency information was provided, thus the prevalence of this variant in the general population could not be determined; the Exome Aggregation Consortium (ExAC) (released Oct 20th, 2014) in 2 of 121336 chromosomes (frequency: 0.0000) from a population of East Asian (2/8642 individuals), and not in European (Non-Finnish or Finnish), Other, African, Latino, South Asian individuals; and, it was identified in ClinVar (classified as a likely benign variant by the Sharing Clinical Reports Project, derived from Myriad reports; classified as uncertain significance by BIC; and classification not provided by Invitae). The Breast Cancer IARC database notes a weak/null probability the variant creates a de novo splice donor at nt 9728 and a low probability of creating a de novo splice acceptor at nt 9736. The p.Pro3243 residue is not conserved in mammals and lower organisms and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The c.9728C>T variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. 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.