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...
Inverted base and amino acid change in Annovar
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)
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1 answer
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).
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LMGTFY: dbSNP rs=1042522
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