VEP currently only annotates HGVSc for variants that overlap the transcript or are within the introns of the transcript. However, there are some clinically significant variants in the regions immediately upstream/downstream of the UTRs of the transcript (for example certain variants in the TERT promoter region which are upstream of the 5'UTR.
So, it would be very useful to be able to annotate HGVSc for variants in the regions immediately upstream/downstream of the UTRs of the transcript (like the variants that get the consequence terms: upstream_gene_variant or downstream_gene_variant). Even if you don't want to implement this as a default feature, it would be very useful to at least implement this feature through an option.
VEP currently only annotates HGVSc for variants that overlap the transcript or are within the introns of the transcript. However, there are some clinically significant variants in the regions immediately upstream/downstream of the UTRs of the transcript (for example certain variants in the TERT promoter region which are upstream of the 5'UTR.
So, it would be very useful to be able to annotate HGVSc for variants in the regions immediately upstream/downstream of the UTRs of the transcript (like the variants that get the consequence terms:
upstream_gene_variantordownstream_gene_variant). Even if you don't want to implement this as a default feature, it would be very useful to at least implement this feature through an option.