A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders

Abstract

We developed a rules‐based scoring system to classify DNA variants into five categories including pathogenic, likely pathogenic, variant of uncertain significance (VUS), likely benign, and benign. Over 16,500 pathogenicity assessments on 11,894 variants from 338 genes were analyzed for pathogenicity based on prediction tools, population frequency, co‐occurrence, segregation, and functional studies collected from internal and external sources. Scores were calculated by trained scientists using a quantitative framework that assigned differential weighting to these five types of data. We performed descriptive and comparative statistics on the dataset and tested interobserver concordance among the trained scientists. Private variants defined as variants found within single families (n = 5,182), were either VUS (80.5%; n = 4,169) or likely pathogenic (19.5%; n = 1,013). The remaining variants (n = 6,712) were VUS (38.4%; n = 2,577) or likely benign/benign (34.7%; n = 2,327) or likely pathogenic/pathogenic (26.9%, n = 1,808). Exact agreement between the trained scientists on the final variant score was 98.5% [95% confidence interval (CI) (98.0, 98.9)] with an interobserver consistency of 97% [95% CI (91.5, 99.4)]. Variant scores were stable and showed increasing odds of being in agreement with new data when re‐evaluated periodically. This carefully curated, standardized variant pathogenicity scoring system provides reliable pathogenicity scores for DNA variants encountered in a clinical laboratory setting.

Consensus Statement on next-generation-sequencing-based diagnostic testing of hereditary phaeochromocytomas and paragangliomas

“…Recognizing that some variants will have more complex requirements for classification, the Study Group recommends following the rules proposed by Richard and colleagues, which combine multiple criteria for classifying variants 63 . Variant classification requires the combination of several criteria, which are described in the following paragraphs 63,64 .…”

The current state of clinical interpretation of sequence variants

“…The uncertain significance category is a default classification for variants lacking sufficient evidence to determine their clinical significance [20••]. Some academic and commercial molecular diagnostic laboratories further subcategorize variants of uncertain significance (VUS) into “leaning pathogenic” or “leaning benign”, if supportive data exist but is insufficient to meet criteria for likely pathogenic or likely benign [30,31]. For example, a variant that segregates with disease in an affected relative and is absent from general population databases may warrant the variant to be classified as VUS “leaning pathogenic”, but is insufficient to classify it as likely pathogenic.…”

Fetal diagnosis of Mowat‐Wilson syndrome by whole exome sequencing

“…Truncations of the protein at locations more distal to this residue have been classified previously as pathogenic (Tyr220*, Ser225*, Gln269* and others). The ZEB2 : p.(Tyr176*) variant was classified as pathogenic according to ACMG guidelines on the basis of being a null variant (PVS1), being de novo (PS2), and being absent in population databases (PM2) (Amendola et al, ; Karbassi et al, ; Nykamp et al, ; Richards et al, ). Pathogenic variants in ZEB2 are implicated in MWS.…”