in conjunction to one previous post concerning ANNOVAR (C: How to select a "representative" transcript in multiple transcript variants from) I would like to ask a specific question concerning the deleteriousness/pathogenicity scores obtained from various annotation tools/databases like SHIFT, CADD etc.-
as for example in ANNOVAR, multiple transcript variants are returned per somatic point mutation, such as the following:
however, single numeric scores are retrieved from the various scoring algorithms-thus, these scores are related from protein changes from "consensus" or representative transcripts from the relative database, or are created in a different way ? and thus, the presence of multiple transcript variants should not affect the pathogenicity of the alteration per se ?
Thank you in advance,