Answers.Body: <p>The answer is you can't see a SNP outside a gene for <code>gnomad</code> because you stated it is <em>exome data</em>. Thus, a minimal definition of the gene is it comprises: introns, exons and a promoter region.</p>
  <p><em>Exome</em> = <em>exon</em> so you downloaded a subsection the gene across the genome.</p>
  <p>To reiterate, you don't have any external allele frequency data outside the gene. However, if your <em>in-house</em> 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 <em>in-house</em> data set comprises however and outside an <em>exon</em> 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.</p>
  <p>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.</p>
  
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Answers.CreationDate: 2022-12-14T15:23:00.637Z
Answers.Text: ♦ 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?
Answers.UserDisplayName: Eliza Romanski
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Answers.CreationDate: 2022-12-14T15:30:04.700Z
Answers.Text: Yes that would resolve the situation.
Answers.UserDisplayName: M__
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Answers.CreationDate: 2022-12-14T14:36:08.017Z
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Answers.LastEditDate: 2022-12-14T14:42:06.707Z
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Body: <p>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):</p>
  <blockquote>
  <p>&quot;No genes were found in this region&quot;</p>
  </blockquote>
  <p>As part of my report question for homework I need to answer this:</p>
  <blockquote>
  <p>&quot;Are the SNPs in your data  that are not in gnomad are outside genes?&quot;,</p>
  </blockquote>
  <p>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?</p>
  <p>I found this in an article:</p>
  <blockquote>
  <p>&quot;<a href="https://medlineplus.gov/genetics/understanding/genomicresearch/snp/" rel="nofollow noreferrer">Single-nucleotide polymorphisms (SNPs) are single base-pair substitutions that occur within and outside genes</a>&quot;</p>
  </blockquote>
  <p>Also found this:</p>
  <blockquote>
  <p>&quot;SNP markers might be selected outside of exomes or the direct cause of a genetic mutation&quot; does this means that it is found in the genome but not exome data in gnomad as it is outside the gene?</p>
  </blockquote>
  <p>Basically, I can't seem to understand what is a SNP outside a gene and can I see this information in gnomad.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-12-14T12:54:22.270Z
Comments.Text: @Community edited hope it is better
Comments.UserDisplayName: Eliza Romanski
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-12-14T21:50:04.770Z
Comments.Text: Cross-posted on biostars: https://www.biostars.org/p/9548287/
Comments.UserDisplayName: Ram RS
Tags: <gene><snp><homework><exome><gnomad>
Title: SNPs location out side the gene
ThreadText: # SNPs location out side the gene
  
  (Asked by: username_0 on 2022-12-14)
  
  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](https://medlineplus.gov/genetics/understanding/genomicresearch/snp/)"
  
  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.
  
  **Tags:** gene, snp, homework, exome, gnomad
  
  > **Comments:**
  > **username_0**: @Community edited hope it is better  
  > **username_1**: Cross-posted on biostars: https://www.biostars.org/p/9548287/  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2022-12-14. Score: 1 | Accepted answer
  
  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.
  
  > **Comments:**
  > **username_0**: ♦ 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?  
  > **username_2**: Yes that would resolve the situation.  
  
  ---
  
  