Variant not annotated by ANNOVAR in the main transcript

Question

[geocarvalho]

Hello, I have a variant in the PMS2 gene that wasn't annotated by ANNOVAR using the main transcript (NM_000535). I'm using the database for hg38 genome.

chr7    6003982 6003982 G   A

PMS2:NM_001322008.2:exon2:c.25C>T:p.R9X,PMS2:NM_001322007.2:exon3:c.25C>T:p.R9X

It is a stop codon but in the main transcript is another non-synonymous variant. Do you know if I can add the other transcript by a parameter from ANNOVAR?

Any help is appreciated. Best regards, George.

[geocarvalho]

Item 10 from ANNOVAR FAQ talks about precedence and other possibilities:

(1) the use of different gene-definition systems ... (4) ANNOVAR uses precedence rules, so if a variant is intronic for one transcript but coding for another transcript, it will be reported as coding only. You need to use -separate argument to show all annotations if this is of interest to you.

I'll give a try to this -separate option.