The transcript is chosen based on the severity of the coding impact, then whether there’s a canonical transcript, and failing that, whichever transcript encodes the longest protein.
On VarSome.com, the user can manually override the default transcript for ACMG classification. For example if the variant has a different coding impact in that transcript it may change the ACMG verdict.
The blue question mark next to the transcript explains why the transcript was automatically selected:
This feature is also available in VarSome Clinical, where you can even define your preferred transcript for annotation of each gene on a global level, which may be quite useful for accreditation and validation purposes.