ClinVar

Description

The BRCA2 p.Ser976Ile variant was identified in 2 of 3116 proband chromosomes (frequency: 0.0006) from individuals or families with breast cancer (Lee_2008_18284688, Weitzel_2005_16030099). The variant was also identified in the following databases: dbSNP (ID: rs276174831) as “With other allele” , ClinVar (as benign by BIC, Invitae, Quest Diagnostics, Sinai Health System, LabCorp, CHEO, GeneDx, and Ambry Genetics, as likely benign by Counsyl and Color Genomics, and as uncertain significance by EGL Diagnostics), Clinvitae (with conflicting interpretations of pathogenicity), COGR (as benign by COGR consensus), LOVD 3.0 (13x), UMD-LSDB (11 x classified as neutral and co-occurring with a pathogenic BRCA1 variant p.Gln1273X), BIC Database (26 x in BIC with no classification). The variant was not identified in Cosmic, MutDB, ARUP Laboratories, Zhejiang Colon Cancer Database. The variant was identified in the Exome Aggregation Consortium (August 8th 2016), and the Genome Aggregation Database (Feb 27, 2017) listed under two different dbSNP identification numbers: rs11571656; rs144862123; in both cases it was identified in 167 of approximately 23980 African population chromosomes (frequency: 0.0069) and was also observed in Latino in 9 of 34204 chromosomes, increasing the likelihood that this may be a low frequency allele without clinical significance. This variant is an in-frame deletion resulting in the removal of a serine (Ser) residue at codon 976; the impact of this alteration on BRCA2 protein function is not known. Although the p.Ser976 residue is not conserved in mammals, four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the p.Ser976Ile variant may impact the protein. However, this information is not predictive enough to assume pathogenicity. One in silico study yielded inconclusive risk predictions for this variant (Lee_2008). The variant occurs outside of the splicing consensus sequence and 1 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, this variant meets our labortory's criteria to be classified as benign.