ClinVar Genomic variation as it relates to human health

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.

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.

The BMPR1A p.Pro145= variant was identified in dbSNP (ID: rs11818239) as “With Benign, Likely benign allele”, ClinVar (classified benign by Ambry Genetics, Illumina, Invitae, Quest Diagnostics Nichols Institute San Juan Capistrano, ARUP, Color, Prevention Genetics and Mayo Clinic; and likely benign by True Health Diagnostics). The variant was identified in control databases in 3757 (239 homozygous) of 277074 chromosomes at a frequency of 0.01 (Genome Aggregation Database Feb 27, 2017, observed in the following populations: African in 3359 (236 homozygous) of 24018 chromosomes (freq: 0.1), Other in 46 of 6458 chromosomes (freq: 0.007), Latino in 269 (2 homozygous) of 34418 chromosomes (freq: 0.008), European Non-Finnish in 74 (1 homozygous) of 126644 chromosomes (freq: 0.0006), East Asian in 1 of 18866 chromosomes (freq: 0.00005), and South Asian in 8 of 30782 chromosomes (freq: 0.0003), while not observed in the Ashkenazi Jewish and European Finnish populations. The p.Pro145= 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 outside of the splicing consensus sequence, 5 bases into exon 7, and 3 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing. However, this information is not predictive enough to assume pathogenicity. In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign.