How to interpret the scores given by G1000, ExAC, Exo, ClinVar Polyphen2, SIFT and Mutation taster provided in the SOPHiA Platform, and compare these values to those provided by the respective databases?
The SOPHiA Platform normalizes the scores provided by the different databases to enable comparisons among the difference sources. For all predictive scores, a value of 1 means likely pathogenic and 0 likely benign irrespective of the database. The scores are transformed as:
“1 – SIFT” score (the original SIFT score is opposite, with 0 being predicted pathogenic and 1 benign)
No transformation (there are two different PolyPhen2 scores, HVAR and HDIV, based on different training sets)
Combination of prediction and score (1 – confident, 0 not confident). The SOPHiA Platform displays the score if the prediction is pathogenic or “1 – score” if the prediction is benign
LRT score (not in spider plot but can be selected in the variant table)
Contains the score and a value omega. The SOPHiA Platform displays “1 – LRT score x 0.5” if omega < 1 or “LRT score x 0.5” if omega ? 1
More detail of such transformations can be found in the dbNSFP database publication: