Effect of Non-Cannonical splice site on impact of variation

Question

[kautilya]

I am using a combination of snpEff and the Loftee plugin for Ensembl VEP to detect Loss of Function(LOF) variations.

However the Loftee plugin marks majority of the snpEff detected LOFs as Low Confidence due to the below given filter:-

NON_CAN_SPLICE_SURR - The LoF falls in an exon whose surround splice sites are non-canonical (not GT..AG).

I dont understand how will a stop gained type of mutation be affected by having non-canonical splice sites around it?

Answer 1

[Emily]

Looking at the documentation, this is what seems to be relevant:

For stop-gained and frameshift variants, LOFTEE removes: [...]

Variants that land in an exon with non-canonical splice sites around it (i.e. intron does not start with GT and end with AG)

It's saying that if an exon appears to be non-canonical, then it might not actually get into a protein, therefore nonsense mutations in that exon are unlikely to affect protein function.