Splice site impact

Question

[Jng]

This is my variant hg19

5-1254700-C-T
TERT:c.3158-80G>A
NM_198253.3

SpliceAI predicts donor site gain (~0.49)

How can I predict what the consequence will be?

Answer 1

[Ared445]

Variant Effect Predictor may be useful: https://www.ensembl.org/info/docs/tools/vep/index.html

[Jng]

Thank you. I found this to be an interesting tool.

Can I know if the consequence will be inframe or out of frame?

Can I determine if the last few exons downstream will be spliced out resulting in a loss of function to the protein?

[Emily]

There is not the biological knowledge to make that prediction