incorrect SO assignment - "exon_loss_variant" for intronic region

KarchinLab / open-cravat

A modular annotation tool for genomic variants

MIT License

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Open EugeneEA opened 6 months ago

EugeneEA commented 6 months ago

Hi, I'm annotating the following variant:

chr15 57989910 CAAAAATGACAGGACGGAGCTTGCAGTGAGCCGAGATTGCGTCACTGCAGTCCGCAGTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAA C

and I'm getting the following results, which says it has a exon loss effect:

Even though it seems to be fully intronic. I also have checked other transcript at that site but seems non of them have an exon in that range

Best, Eugene

RachelKarchin commented 2 months ago

Sorry for slow response. We are looking into this issue and it is in our queue.