Hi all,
I came across an SNP rs number merged to another SNP rs number with different chromosome coordinates. I would like to know whether both can be considered as significant or the latest reference number allotted to be considered.
Below are the details for the same:
Dbsnp - rs730880339 has merged into rs730880334 [Homo sapiens].
rs730880339 - chr7:55248998-55248999 (the amino acid position when checked in IGV is 766)
rs730880334 - chr7:552489008-55249009 (the amino acid position when checked in IGV is 769)
As EGFR exon 20 insertion is important in considering the therapeutic benefits for lung cancer patients, So I need to understand which snp_id and chromosome coordinate to be considered for the same.
this variant inserts 9 bases. These 9 bases represents a duplication of 9 bases which are in the reference. No one can clearly say where this bases were inserted. Before or after the reference bases?
For the protein translation this doesn't matter. But human has a problem on how to describe it and makes it comparable. There is a technique called normalization which should enable this. One criteria is to locate a variant at the most left position within the reference sequence. But if we call a variant a duplication, the convention is to locate the insertion of bases right after the bases that will be repeated.
To summarize it: Both description behind the given SNP Ids are correct, as they describe the same insertion of bases which lead to the same changes in the protein sequence. For harmonization reasons these snp ids get merged.