Inverted base and amino acid change in Annovar

Question

[user31888]

I detected the following variant and annotated it with Annovar (using hg19 ref. genome):

Chr: 17
Start: 7579472
Ref.: G
Alt: C
dbSNP: rs1042522
AAChange.ensGene: ENSG00000141510:ENST00000359597:exon3:c.C215G:p.P72R

The AAChange fits with the dbSNP entry (both C>G and Pro>Arg), but differs with my Ref. and Alt (they are inverted). Also when I load my ref. genome into IGV, the position falls into a CGG codon that codes for Arg. Replacing the G by C produces a CGC codon that also codes for a Arg, not a Pro.

Why the annotation is inverted compared to my Ref./Alt.?

* EDIT *

Wildtype:
sense       CGG
              ^
antisense   GCC     ==>     Pro

Mutant:
sense       CGC
              ^
antisense   GCG     ==>     Ala

(the "^" indicates the mutation position on the sense strand, i.e. 17:7579472)

Answer 1

[harold.smith.tarheel]

You're looking on the wrong strand. This gene is in the antisense orientation on the reference. The reference codon is actually 'CCG' (Pro), and the SNP is 'CGG' (Arg).

[user31888]

Harold, it makes sense for the codon encoding Pro but not for the mutant that would code for Ala in this case (see edit on the OP). I am clearly missing something...

[harold.smith.tarheel]

LMGTFY: dbSNP rs=1042522

[user31888]

I saw that. Does not answer the question

[harold.smith.tarheel]

Actually, it does. The SNP is in the second nucleotide of the codon, not the third as your edit indicates. Your positioning may be off due to zero-based vs one-based counting.