how do you get an IN-FRAME deletion stop gain variant?

Question

[jon.klonowski]

I was looking through annotaitons for variants in my genomics data and I saw some variants being labeled by VEP derived ensembl consequence as "stop_gained&inframe_deletion"

How do you get a stop gain from an inframe deletion? It makes sense for an inframe insertion (the insertion is a stop codon) or an out of frame insertion, but not an inframe deletion...

Here are some rs examples: rs781637300, rs751061041, rs1282390381

Answer 1

[jon.klonowski]

I think I can see it. It is when the deletion causes the bases to fall back in place such that the a stop codon is generated but technically the reading frame is preserved, as the following triplets - IF READ - would be unchanged.

[Ben_Ensembl]

Hi jon.klonowski,

Just to confirm that you're own answer is correct. In each of the examples you provided, the variants were either INDELs or DELETIONs where the number of bases deleted is divisible by 3 but a STOP codon is created.

This is probably easiest to see in the 'Genes and Regulation' page of the Variant tab. E.g: https://www.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;r=2:96114574-96115583;v=rs751061041;vdb=variation;vf=375885903

[jon.klonowski]

yes, thank you! Despite understanding the concept, it took a bit to figure out that this is what is going on from just looking at annotations .