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.

Variant summary: NBN c.2220T>C alters a non-conserved nucleotide resulting in a synonymous change. 5/5 computational 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 0.00056 in 281422 control chromosomes, predominantly within the East Asian subpopulation at a frequency of 0.0078 in the gnomAD database. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 60 fold of the estimated maximal expected allele frequency for a pathogenic variant in NBN causing Hereditary Breast and Ovarian Cancer phenotype, strongly suggesting that the variant is a benign polymorphism found primarily in populations of East Asian origin. Though the variant, c.2220T>C, has been reported in the literature in East Asian individuals affected with breast cancer (Kim 2015), it was also found in several healthy controls (Momozawa 2018). A large case-control association study involving unselected breast cancer patients and controls of Japanese ancestry concluded that the variant is benign (Momozawa 2018). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as benign (1x) / likely benign (1x). Based on the evidence outlined above, the variant was classified as benign.

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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

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 NBN p.Ala740= variant was identified in 47 of 14,208 proband chromosomes (frequency: 0.003) from individuals with breast cancer and was present in 117 of 47,460 control chromosomes (frequency: 0.002) from healthy individuals (Momozawa 2018). The variant was identified in dbSNP (rs147494981) as “with likely benign allele”, ClinVar (classified as benign by Invitae and GeneDx and likely benign by Color and Ambry Genetics) and LOVD 3.0 (observed 5x). The variant was identified in control databases in 157 of 281,422 chromosomes at a frequency of 0.0006 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: East Asian in 156 of 19,936 chromosomes (freq: 0.008 increasing the likelihood this could be a low frequency benign variant), Other in 1 of 7180 chromosomes (freq: 0.0001), while the variant was not observed in the African, Latino, Ashkenazi Jewish, Finnish, European and South Asian populations. The p.Ala740= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. The variant occurs at a non-highly conserved nucleotide outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) 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.