How does SnpEff discriminate between transcripts?

Question

[Maxime]

Hi,

Looking for example at this line of a VCF file :

1   155322556   .   C   G   [...] ;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cCg|R2436P|2964|ASH1L||CODING|NM_018489.2|17|1) [...]    GT:AO:DP:GQ:PL:QA:QR:RO 0/0:11:55:74:0,40,100:66:917:44 0/0:4:35:99:0,81,100:8:868:31   0/1:12:32:0:1,0,100:91:658:20   0/1:16:37:16:100,0,100:216:630:21

So this mutation R2436P affect gene ASH1L on this transcript NM_018489.2 which is the transcript 2.

How does SnpEff knows it doesn't affect the transcript 1 leading to the canonical isoform as shown on Uniprot ? : https://www.uniprot.org/uniprot/Q9NR48#Q9NR48-1

Thank you,

Maxime

Answer 1

[Pierre Lindenbaum]

EFF= is for the old version of snpEff. you should update your software.

Snpeff produces an ouput for each transcript. more than one annotation at a locus in SnpEff output? ; How to Get only one annotation with the SnpEff annotation? ; ...