SNPEff output meaning

Question

[simone.castellana]

Hi everyone,

I wonder if anyone can help understand this SNPEff output:

chr pos strain  gene_name   type    effect_impact   ref alt codon_change    amino_acid_change
1   20136579    6911    RAP2.12  frameshift_variant+stop_lost   HIGH    TG  T   tga/    p.Ter357fs/c.1070delG

What I'd like to understand is what the 'amino_acid_change' means with: p.Ter357fs/c.1070delG

Sorry if the question doesn't sound clear, but I'm new here.

Thanks for your help

[Hamid Ghaedi]

This is a more genetic question than a bioinformatic related question. Anyway I do recommend checking the website for Sequence Variant Nomenclature available here: https://varnomen.hgvs.org/. There, under DNA section check for deletion : https://varnomen.hgvs.org/recommendations/DNA/variant/deletion/

Answer 1

[evolozzy]

It is actually TGA, which is the stop codon, and G is deleted so it says deletion of G on Ter(minating) sequence.