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 criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

This alteration is classified as 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 BARD1 p.Cys557Ser variant was identified in 466 of 24464 proband chromosomes (frequency: 0.019) from individuals or families with breast and ovarian (hereditary and sporadic) cancers, and was identified in 263 of 16634 chromosomes (frequency: 0.016) from healthy individuals (Ding 2011, Ghimenti 2002, Gonzalez_Hormazabal 2012). A meta-analysis done to assess if this variant was associated with increased risk of breast cancer found no evidence to support this association except in women with a strong family history where carriers were found to have a 3.4-fold increase of breast cancer risk (Gonzalez_Hormazabal 2012). In an Italian study looking at BRCA1 and BRCA2 negative HBOC families, the variant segregated with disease in 1 family, and through linkage anlaysis both BARD1 and BRCA2 were linked to disease in the family (Ghimenti 2002). Analysis of unselected breast and ovarian tumors identified the variant in an ovarian tumour in hemizyous state, with functional assays indicating it may contribute to cancer phenotype (Sauer 2005). The variant was also identified in dbSNP (ID: rs rs28997576) as “Other”, ClinVar (classification benign by GeneDx, Ambry Genetics, Invitae, Color Genomics Inc., likely benign by Illumina, and as risk factor by OMIM), and Zhejiang Colon Cancer Database (9X) and not in Cosmic and MutDB databases. The variant was identified in control databases in 4197 of 277016 (55 homozygous) chromosomes at a frequency of 0.015 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017), seen in the following populations at a frequency greater than 1%: Ashkenazi Jewish* in 238 of 10146 chromosomes (freq: 0.023), European (Non-Finnish) in 2914 of 126608 chromosomes (freq: 0.023), Other in 98 of 6456 chromosomes (freq: 0.015), and South Asian in 414 of 30782 chromosomes (freq: 0.013). The p.Cys557 residue is not conserved in mammals and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out 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 although we would lean towards a more benign role for this variant. This variant is classified as likely benign.