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