I found a variant which is not reported in gnomAD or ExAC, but still has an rs. Should I consider it as a novel variant?
when can I say that ceratin variant is novel?
If it has an rs# then it must have been identified and given an ID. Search in ncbi snpdb and see if it has frequencies in the 1000 genome project or other population studies, and the same website has ExAc as well. It might be novel in its association with a phenotype you are studying, but if it has an id then it is not "never reported" i.e. novel.
Rabeah Al-Temaimi So, when can I say that a variant is novel?
Just if it has not an rs? or there are other specific criteria?
You call it novel if it has never been reported before in any format, that is the only criteria. However, variants can be reported without an rs#. For example, very rare genomic missense variants are usually reported by their genomic location and change (ex. g.1233G>C, or coding DNA c.233G>C) without having an rs#, or coding variants by their protein change (p.Glu44Asp). Variants other than missense may also have location representation in protein or gDNA, or cDNA. So, best approach is to see if it has an rs# on SNPdb (It has ExAC, GenomAD, and 1000genomes), then if not check in UCSC genome browser for specific location and see if any variants have been reported. Lastly, do a pubmed AND google search for the change on the DNA level, cDNA (coding) level, and protein if present and see if it has ever been reported before in a publication. Usually if it is a disease variant I would also check disease specific genetic respository databases. I rotated as a variant analyst for a large US genetic diagnostics company so this was the preliminary method I established for them. Hope this clears things up for you.
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