Hi, I have question about annotation by Annovar. It is a little bit confusing for me now when I need to identify variants which are potential to change the function of gene or protein.
Annovar produces one table exonic_variant_function table and variant_function table. The first table lists all variants that are located in exonic coding region which could change gene function but second table lists all variants that are located in region close to exon or exon/intron boundary.
In the second variant annotation table made by annovar software. it produces variants which have been called as the "exonic" and they are explained as " here refers only to coding exonic portion" or "variant overlaps a coding exon ". Why these variants are made in Second table but not exonic variant function table??? what does "exonic" here different from "silent mutation"?
Also, "splicing" is explained as variant that is within 2-bp away from an exon/intron boundary by default and "exonic splicing" is explained as a variant within exon but close to exon/intron boundary. Is that mean exonic splicing has low possibility to induce transcript alternative comparing with "splicing"? Not very clear here.
It is so hard to neglect these "exonic" or "exonic splicing" variants or not without no worry about losing real mutation.