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Inverted base and amino acid change in Annovar
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14 months ago
user31888 • 60
United States

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)
annovar • 724 views
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13 months ago
United States

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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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...

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I saw that. Does not answer the question

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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.

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