How to find refgene location for SNPs?

Question

[MAPK]

I have some SNPs that I need to find refgene location (non-synonymous, ncRNA_exonic,splicing, etc) given the chr: position:REF:ALT. I have tried VEP tool, but that does not give me what I want.

I have these SNPs:

chr15:72105885:G:A # and I want: nonsynonymous SNV
chr16:1115931:C:G # and I want: ncRNA_exonic

Answer 1

[venu]

ANNOVAR Package.

If your input file is input.vcf, the output file input.vcf.variant_function will have this information for each variant.

[MAPK]

The SNPs I have were already passed through annovar and have "unknow" location for those SNPs. What does "unknown" mean? Is there anything else I can use to get refgene location (I don't want to use ensemble)?

[venu]

In the provided link, go down and find rule 4

If a transcript maps to multiple locations, all as "coding transcripts", but none has a complete ORF, then this transcript will not be used in exonic_variant_function annotation and the corresponding annotation will be marked as "UNKNOWN".

[MAPK]

Thanks Venu. Another question I have is some of the SNPs are labelled as Unknown by annovar, but ensemble has identified as nonsynonymous SNV. What is difference between these two?

[nuratikah_norazhar]

Hi, sorry to interrupt your both conversation. I'd like to ask an almost similar question. All of my variants that undergo the WES, was completely annotated in Annovar. however, some of the variants were denoted as a dot (.) and "Unknown" for the Exonic Function RefGene and Exonic FunctionKnownGene, while the other variants were annotated as frameshift, synonymous etc.

so, what does that mean for both dot (.) and "Unknown"? thanks in advance!