In terms of variant function, VarSome Clinical annotates variants against all the transcripts available (Ensembl and Refseq), and shows the results in the Function column when browsing results:
However, for the Germline Variant Classification, as a part of the annotation of variants, VarSome Clinical considers only one transcript - by default the transcript with:
- the most severe coding impact,
- otherwise the MANE Select transcript
- if the above is not available, the longest canonical transcript
- otherwise, the MANE Plus transcript
- failing that, the longest transcript
- and finally, the RefSeq transcript
For Ensemble transcripts, all must have TSL  = 1 or null.
In addition to that, there is an option for you to use your preferred list of transcripts for annotations as well. Please, note that this option is not available for users evaluating VarSome Clinical during the free trial period.
What you need to do is to send us the list of transcripts you wish to annotate the variants with, and we will let you know as soon as it is available for your analyses.