ClinVar

Description

The BRCA2 p.Val2969Met variant was identified in 6 of 9554 proband chromosomes (frequency: 0.001) from individuals or families with hereditary breast and ovarian cancer and was not identified in 80 control chromosomes from healthy individuals (Akbari 2011, Borg 2010, Soegaard 2008, Stegel 2011, Kluska 2015). The variant was also identified by our laboratory in 1 individual with hereditary breast and ovarian cancer. The variant was also identified in dbSNP (ID: rs59004709) as “other”, Clinvitae database (as benign), Fanconi Anemia Mutation Database -LOVD (3x, as predicted neutral 2x and predicted deleterious 1x), LOVD-IARC database (as not pathogenic), ARUP Laboratories BRCA Mutations Database (as not pathogenic), the ClinVar database (as benign, reviewed by an expert panel), GeneInsight COGR database (as “benign”, “likely benign”, and “unknown significance”, by clinical laboratories), the BIC database (24x with unknown clinical importance), and UMD (23x with a “likely neutral” classification). This variant was identified in the 1000 Genomes Project in 3 of 5000 chromosomes (frequency: 0.0006), NHLBI GO Exome Sequencing Project in 2 of 8600 European American alleles and 1 of 4406 African American alleles, and in the Exome Aggregation Consortium database (March 14, 2016) in 49 of 120422 chromosomes (freq. 0.0004) in the following populations: European (Non-Finnish) in 41 of 66196 chromosomes (freq. 0.0006), European (Finnish) in 4 of 6614 chromosomes (freq. 0.0006), and African in 4 of 10180 chromosomes (freq. 0.0004), but was not seen in East Asian, Latino, South Asian and other populations, increasing the likelihood this could be a low frequency benign variant. There is conflicting information in the literature. Two in-silico functional studies suggest this variant is predicted neutral (Easton 2007, Lindor 2012), while two others suggest the variant is likely deleterious (Karchin 2008, Kluska 2015). The p.Val2969 residue is conserved in mammals 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 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 uncertain significance.