ClinVar Genomic variation as it relates to human health

Variant summary: The EFEMP2 c.1188C>T (p.Ser396Ser) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. Mutation taster predicts a damaging outcome for this variant. 3/5 splice prediction tools predict a significant impact on normal splicing. ESE finder predicts that this variant may create a new binding site for SC35. However, these predictions have yet to be confirmed by functional studies. This variant was found in 240/120628 control chromosomes from ExAC, predominantly observed in the European (Finnish) subpopulation at a frequency of 0.011343 (74/6524). This frequency is about 101 times the estimated maximal expected allele frequency of a pathogenic EFEMP2 variant (0.0001118), suggesting this is likely a benign polymorphism found primarily in the populations of European (Finnish) origin. Similar frequency in European (Finnish) subpopulation (0.01098; 283/25780 chromosomes) has also been detected in gnomAD database, including 2 homozygotes. One clinical diagnostic laboratory (via ClinVar) has classified this variant as uncertain significance without evidence to independently evaluate. To our knowledge, this variant has not been published in affected individuals in literature. Taken together, this variant is 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance 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.

EFEMP2: BP4, BP7

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).