UTRannotator ignores consequences containing 5_prime_UTR_variant

[dennishendriksen]

VEP annotates some 5_prime_UTR_variant variant features with additional consequences, for example: X 153297660 G>T on GRCh37 will be annotated with CSQ=T|splice_region_variant&5_prime_UTR_variant|.... These variant variant consequences seem to be ignored by the VEP UTRannotator plugin. Possibly because of an == check? Is this behavior intentional?

[nickywhiff]

Hi, thank you for your comment. This is definitely not intentional behaviour. We can't seem to replicate an error with variants annotated with multiple features. In our hands they are annotated as we would expect. I also tried manually annotating your example variant above using VEP on GRCh37 and do not get any annotation of 5_prime_UTR_variant on any transcripts. Perhaps you have another example I can check?

[dennishendriksen]

Hi @nickywhiff, thank you for the quick reply! Would you mind checking 11:57365723 T>C on your side? I'm running VEP v105 in combination with other plugins, based on your reply it might be that the issue is caused by another plugin resulting in the skipping of UTRannotator.