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I downloaded exome data from gnomad to get the allele frequency of some SNPs that I'm analyzing. The SNPs are from external resource. Some SNPs (in my data) are not present in the exome data (in gnomad):

"No genes were found in this region"

As part of my report question for homework I need to answer this:

"Are the SNPs in your data that are not in gnomad are outside genes?",

What does it mean SNP outside genes? Does it mean that they are not in the exome data but in the genome data on gnomad?

I found this in an article:

"Single-nucleotide polymorphisms (SNPs) are single base-pair substitutions that occur within and outside genes"

Also found this:

"SNP markers might be selected outside of exomes or the direct cause of a genetic mutation" does this means that it is found in the genome but not exome data in gnomad as it is outside the gene?

Basically, I can't seem to understand what is a SNP outside a gene and can I see this information in gnomad.

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    $\begingroup$ @Community edited hope it is better $\endgroup$ Commented Dec 14, 2022 at 12:54
  • $\begingroup$ Cross-posted on biostars: biostars.org/p/9548287 $\endgroup$
    – Ram RS
    Commented Dec 14, 2022 at 21:50

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The answer is you can't see a SNP outside a gene for gnomad because you stated it is exome data. Thus, a minimal definition of the gene is it comprises: introns, exons and a promoter region.

Exome = exon so you downloaded a subsection the gene across the genome.

To reiterate, you don't have any external allele frequency data outside the gene. However, if your in-house data set is whole genome data, i.e. for making your SNP calls then most of these SNPs will be outside the exon (thats a result of comparative selection pressure). So the answer is yes. It isn't clear what the in-house data set comprises however and outside an exon does not necessarily mean its outside the gene. A lot of mutations will occur within introns (which is outside the exon but still within a gene), but in addition more mutation will occur in intergenic regions, i.e. completely outside the exon + intron + promoter. In this sense the question seems to possibly lack clarity.

To be honest, questions on bioinformatic practicals are often after-thoughts to the core activity, so I wouldn't worry too much about the semantics.

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    $\begingroup$ ♦ thank you for the detailed answer. so if I understand correctly if instead of looking the exome data I would look at the whole genome data in gnomad that would be looking outside the gene? $\endgroup$ Commented Dec 14, 2022 at 15:23
  • $\begingroup$ Yes that would resolve the situation. $\endgroup$
    – M__
    Commented Dec 14, 2022 at 15:30

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