Quantifying prediction of pathogenicity for within-codon concordance (PM5) using 7541 functional classifications of BRCA1 and MSH2 missense variants

Abstract

Conditions and thresholds applied for evidence weighting of within-codon concordance (PM5) for pathogenicity vary widely between laboratories and expert groups. Because of the sparseness of available clinical classifications, there is little evidence for variation in practice. Methods: We used as a truthset 7541 dichotomous functional classifications of BRCA1 and MSH2, spanning 311 codons of BRCA1 and 918 codons of MSH2, generated from large-scale functional assays that have been shown to correlate excellently with clinical classifications. We assessed PM5 at 5 stringencies with incorporation of 8 in silico tools. For each analysis, we quantified a positive likelihood ratio (pLR, true positive rate/false positive rate), the predictive value of PM5-lookup in ClinVar compared with the functional truthset. Results: pLR was 16.3 (10.6-24.9) for variants for which there was exactly 1 additional colocated deleterious variant on ClinVar, and the variant under examination was equally or more damaging when analyzed using BLOSUM62. pLR was 71.5 (37.8-135.3) for variants for which there were 2 or more colocated deleterious ClinVar variants, and the variant under examination was equally or more damaging than at least 1 colocated variant when analyzed using BLOSUM62. Conclusion: These analyses support the graded use of PM5, with potential to use it at higher evidence weighting where more stringent criteria are met.

Evaluating the use of paralogous protein domains to increase data availability for missense variant classification

“…4 ), which would allow PM5 to be applied at a reduced weighting to an additional 14% of variants for which the standard PM5 analysis is not applicable, increasing the sensitivity from 0.27 to 0.41. Consistent with other studies [ 42 ], we also note the higher likelihood ratio when restricting ClinVar variants to those with high REVEL scores, further supporting the graded use of PM5. It should be noted that there was no manual classification of ClinVar variants in our analysis, which is contrary to the current stipulations of the guidelines specifying that variants at the same position must be classified manually and established to be pathogenic.…”

Quantitative thresholds for variant enrichment in 13,845 cases: improving pathogenicity classification in genetic hearing loss

“…Importantly, we recommend that the PS4 criteria is only of utility for providing evidence toward pathogenicity and not toward benignity, as the FP rate is generally low for all proposed PS4 thresholds whist the FN rates are generally high. This recommendation is consistent with the conclusions drawn in the study by Lucy Loong and colleagues, which emphasized the role of the PM5 metric in providing evidence for pathogenicity rather than benignity [ 40 ].…”

EMQN best practice guidelines for genetic testing in hereditary breast and ovarian cancer

“…Where reclassification is likely to change clinical management i.e. from VUS to likely pathogenic (LP) or LP to VUS, and particularly if the evidence is not publicly available, notification should be provided to relevant other diagnostic laboratories and appropriate healthcare professionals to ensure consistent patient management [ 55 ].…”

“…If the reclassification of a variant alters the clinical significance (i.e. from VUS to LP/LP to VUS), laboratories must assess if a reissue of a report to the referring consultant of the proband is required [ 55 ]. 50.…”