Custom transcript for annotation

Regarding 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, VarSome Clinical considers only one transcript for annotation. By default this is the the transcript with:

1. the most severe coding impact,
2. otherwise the MANE Select transcript
3. if the above is not available, the longest canonical transcript
4. otherwise, the MANE Plus transcript
5. failing that, the longest transcript
6. and finally, the RefSeq transcript

For Ensembl transcripts, all must have TSL [1] = 1 or null.

There is a new group setting available that allows you to always annotate with the MANE transcript. When enabled, this setting overrides the default hierarchy described above, ensuring that the MANE transcript is consistently prioritized for your group's analyses. 

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 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 analysis.

The list should be a tab-delimited file with the gene ID and the corresponding transcript:

ABL1<tab>NM_005157.6
ASXL1<tab>NM_015338.6
BCOR<tab>NM_001123385.2