I'm using SnpEff 4.3i with the latest hg38 database (from 2016-10-27 on Sourceforge).
Some of the transcripts in the annotated output have an extra dot and number, e.g. NM_033467.3.2 (example below). I wasn't able to find documentation on what this extra number means, and it doesn't seem to be standard for Refseq IDs. Anyone have a clue?
chr1 2592284 . C T 91.0 PASS SNVSB=-8.2;SNVHPOL=5;ANN=T|intron_variant|MODIFIER|MMEL1|MMEL1.2|transcript|NM_033467.3.2|protein_coding|21/23|c.2068-257G>A|||||| GT:GQ:GQX:DP:DPF:AD 0/1:124:91:24:5:13,11