snpEff predicts stop_gained, but SNP wouldn't produce a stop codon

Question

[Nadine]

Hi,

I did a variant analysis with gatk and used snpEff to annotate the variants. On one position snpEff annotates the effect as stop_gained. But when I visualize this position there is no new stop codon due to the variant. What could the reason for this be?

Only way I could see a new stop would be the opposite strand combined with a reading frame shift making it a TAG. Could this be the reason for this prediction?

Thanks for any help, Best,

Answer 1

[Istvan Albert]

It all depends on the reading frame - there are six reading frames, you need to visualize the feature, where it starts and on which strand it is.