Ambiguous SNP function in dbSNP

Question

[GabrielMontenegro]

I am trying to explore the function of some SNPs and I was using the dbSNP website to check this. I found that on some SNPs the function is ambiguous. For instance for this SNP rs4693 , on the GeneView tab the function is either cds-synon or UTR3 and with different accession numbers.

Which function should I trust?

[Floris Brenk]

Genes can have different isoforms which is true for rs4693. The gene NXF1 has more than 10 isoforms according to gencode v19. So depending on the amount of SNPs you have, you could check manually which isoform is highest expressed one in your target tissue/region and use that isoform as leading for SNP functionality. However when you have large amount of SNP data general consensus is the use of annovar or kggseq and annotate the SNPs from there by default (which isn’t necessary the proper isoform indeed).

[GabrielMontenegro]

Thanks for the reply. Yes, I have actually a lot of SNPs, in that case how can I know the function according to annovar or kggseq on dbSNP?

[Floris Brenk]

Gene feature:

http://statgenpro.psychiatry.hku.hk/limx/kggseq/doc/UserManual.html#GeneFeatureFiltering

or even

Functional annotation:

http://statgenpro.psychiatry.hku.hk/limx/kggseq/doc/UserManual.html#FunctionalAnnotation

Answer 1

[Czh3]

The function annovar given is ordered by splicing,exonic->ncRNA,utr5,utr3->intronic...

Value          Default       Explanation
               precedence
exonic         1             variant overlaps a coding exon
splicing       1             variant is within 2-bp of a splicing junction (use -splicing_threshold to change this)
ncRNA          2             variant overlaps a transcript without coding annotation in the gene definition (see Notes below for more explanation)
UTR5           3             variant overlaps a 5' untranslated region
UTR3           3             variant overlaps a 3' untranslated region
intronic       4             variant overlaps an intron
upstream       5             variant overlaps 1-kb region upstream of transcription start site
downstream     5             variant overlaps 1-kb region downtream of transcription end site (use -neargene to change this)
intergenic     6             variant is in intergenic region