Hello,
I was running Annovar to annotate snps and indels. While checking the assigned information of potentially pathogenic mutations I discovered that rs number from avdbsnp144 is not compatible with chromosome coordinates. Example below.
48878115 48878117 CCG - exonic RB1 rs587778823
According to dbSNP rs587778823 represents 48878120-48878122 coordinates, and it's assigned as "with pathogenic allele". But this is not my deletion!
So, I was checking what could be wrong. I found that deletion with presented coordinates (48878115-48878117) has rs760927237 (not pathogenic!). But it is not what Annovar annotated.
First, I thought that maybe it's the reverse and forward strand differences -- no, RB1 is on forward strand.
Second, I looked at hg19_avsnp144.txt downloaded from annovar web page. And here is what I found:
13 48878115 48878115 CCG - rs587778823
13 48878115 48878115 CCG - rs760927237
Can anybody explain why deletion has two rs number with different clinical significance?
Is it possible to make annovar write in output both rs numbers?
I would appreciate for any help,
Agata
