Annotate Transcripts

This algorithm annotates variants against overlapping transcripts. The algorithm produces a number of fields for each variant. These fields are documented in the field documentation produced by the computation.


An gene source is needed to run the algorithm.


  • Only annotate verified mRNA transcripts: If checked, only verified transcripts will be included.
  • Include splice site predictions: If checked, includes 4 algorithms and a summary voting of these algorithms on whether the variant disruptis a nearby canonical splice site.
  • Amino Acid Notation: Amino acids can be represented as either three letter or one letter abbreviations.
  • Splice Site Boundaries: The distances used to classify splice site boundaries can be adjusted as needed.
    • Splice Donor Distance: Default is 2 bp
    • Splice Acceptor Distance: Default is 2 bp
    • Splice Region Exonic Distance: Default is 3 bp
    • Splice Region Intronic Distance: Default is 8 bp
  • Preferred Transcript(s): A list of transcripts that should be preferred as the clinical relevant transcript.


Three column groups will be created. A summary group, which collapses overlapping annotations to produce a clinically relevant annotation. Second, a full annotation which details the interactions for each transcript-variant pair. Finally, a set of columns containing the information in the underlying source.

If multiple transcripts overlap the variant then the results will be joined together in a list for each field. If a variant is intergenic non applicable fields will be filled in with missing values.

Splice Site Detection Boundaries

Callable splice site positions for each algorithm:

  • MaxEntScan
    • Donor: -3, +6
    • Acceptor: -18, +3
  • GeneSplicer
    • Donor/Acceptor: -80, +80
  • NNSplice
    • Donor: -7, +8
    • Acceptor: -21, +20
  • PWM
    • Donor: -3, +4
    • Acceptor: -12, +1