Answers.Body: <p><a href="https://varsome.com" rel="nofollow noreferrer">VarSome</a> allows you to annotate any variant, including non coding ones. While ACMG classification will not be available if the variant isn't in a gene's transcript (the ACMG criteria are only applicable to variants in transcribed regions), non-coding variants in transcripts will be fully annotated. For example, if you look up variant <a href="https://varso.me/JyHZ" rel="nofollow noreferrer">chr17-41197559-G-T</a> which is a non-coding variant found in the UTR of one of the transcripts of BRCA1, you will get a <em>lot</em> of information (probably best to click on the link, the image has a <em>lot</em> of data):</p>
  
  <p><a href="https://i.sstatic.net/AsaDw.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/AsaDw.png" alt="VarSome screenshot"></a></p>
  
  <p>For non-coding variants that don't fall in any transcript, you can still get frequency data, when available, as well as DANN pathogenicity predictions, GERP score, an overview of the genomic regions and other variants and/or srtuctural variants that can be found around the region, and any community annotations that may have been submitted by other users. </p>
  
  <p><a href="https://varsome.com/information/varsome-api-info/" rel="nofollow noreferrer">There is also an API</a> you can use to automate the annotation, and <a href="https://varsome.com/editions/" rel="nofollow noreferrer">VarSome Pro</a> that lets you annotate an entire VCF file, but those are both paid services.</p>
  
  <hr>
  
  <p><strong>Disclaimer</strong>: I work for the company behind VarSome. </p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-08-27T12:15:21.097Z
Answers.Text: This looks interesting but *yikes* I don't think it would be much of use in my case since automating the annotation is in my needs. Thanks though.
Answers.UserDisplayName: user324810
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-08-27T12:23:30.590Z
Answers.Text: @Law yeah, the API and/or the Pro version where you can send VCFs would probably be helpful for you, but those aren't free. I thought I'd mention them in case you do have a budget.
Answers.UserDisplayName: terdon
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-08-27T09:17:30.970Z
Answers.LastActivityDate: 2019-08-27T09:17:30.970Z
Answers.UserDisplayName: terdon
Body: <p>I would like to ask if there are some known databases that allows to annotate non-coding mutations in a given region for the human genome?</p>
  
  <p>Preferably, if the database is downloadable so I am able to automatize the processes of annotation.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-08-27T09:07:39.093Z
Comments.Text: What do you mean with non-coding mutations? SNPs? Check dbSNP.
Comments.UserDisplayName: benn
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-08-27T09:59:47.690Z
Comments.Text: What sort of annotations are you looking to include? Ensembl's VEP is great for annotation, and can include many different annotations applicable to both coding and non coding regions, e.g. minor allele frequency, conservation, pathogenicity predictions through CADD (via a plugin) and many other things
Comments.UserDisplayName: JenG
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-08-27T12:09:11.713Z
Comments.Text: @benn yes SNPs, I know about dbSNP, I wanted to know if there are other known databases !
Comments.UserDisplayName: user324810
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-08-27T12:10:33.757Z
Comments.Text: @JenG I have VEP installed on my cluster ! but CADD also comes with dbSNP plugin, but thanks I will have a look on it
Comments.UserDisplayName: user324810
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-08-27T13:29:10.473Z
Comments.Text: We could give you better answers if you explained what sort of information you are looking for. What kind of "annotating" do you need?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-08-27T14:47:21.237Z
Comments.Text: Agreed. dbSNP can easily be downloaded and integrated into an automated annotation pipeline. Please provide more details about what precisely you're looking for.
Comments.UserDisplayName: Daniel Standage
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-08-28T08:20:14.987Z
Comments.Text: Sorry for the late reply. I am looking to annotate non-coding mutations (introns, UTRs, etc... but also exons if possible) coming into active enhancers of the human genome of the pancreatic islets. For example, if a mutation comes into an active enhancer in an intron, what kind of predicted impact would that mutation do ?
Comments.UserDisplayName: user324810
Tags: <database><sequence-annotation><mutations><non-coding>
Title: Are there databases to annotate non-coding mutations?
ThreadText: # Are there databases to annotate non-coding mutations?
  
  (Asked by: username_0 on 2019-08-27)
  
  I would like to ask if there are some known databases that allows to annotate non-coding mutations in a given region for the human genome?
  
  Preferably, if the database is downloadable so I am able to automatize the processes of annotation.
  
  **Tags:** database, sequence-annotation, mutations, non-coding
  
  > **Comments:**
  > **username_1**: What do you mean with non-coding mutations? SNPs? Check dbSNP.  
  > **username_2**: What sort of annotations are you looking to include? Ensembl's VEP is great for annotation, and can include many different annotations applicable to both coding and non coding regions, e.g. minor allele frequency, conservation, pathogenicity predictions through CADD (via a plugin) and many other things  
  > **username_0**: @username_1 yes SNPs, I know about dbSNP, I wanted to know if there are other known databases !  
  > **username_0**: @username_2 I have VEP installed on my cluster ! but CADD also comes with dbSNP plugin, but thanks I will have a look on it  
  > **username_3**: We could give you better answers if you explained what sort of information you are looking for. What kind of "annotating" do you need?  
  > **username_4**: Agreed. dbSNP can easily be downloaded and integrated into an automated annotation pipeline. Please provide more details about what precisely you're looking for.  
  > **username_0**: Sorry for the late reply. I am looking to annotate non-coding mutations (introns, UTRs, etc... but also exons if possible) coming into active enhancers of the human genome of the pancreatic islets. For example, if a mutation comes into an active enhancer in an intron, what kind of predicted impact would that mutation do ?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2019-08-27. Score: 1
  
  [VarSome](https://varsome.com) allows you to annotate any variant, including non coding ones. While ACMG classification will not be available if the variant isn't in a gene's transcript (the ACMG criteria are only applicable to variants in transcribed regions), non-coding variants in transcripts will be fully annotated. For example, if you look up variant [chr17-41197559-G-T](https://varso.me/JyHZ) which is a non-coding variant found in the UTR of one of the transcripts of BRCA1, you will get a *lot* of information (probably best to click on the link, the image has a *lot* of data):
  
  [![VarSome screenshot](https://i.sstatic.net/AsaDw.png)](https://i.sstatic.net/AsaDw.png)
  
  For non-coding variants that don't fall in any transcript, you can still get frequency data, when available, as well as DANN pathogenicity predictions, GERP score, an overview of the genomic regions and other variants and/or srtuctural variants that can be found around the region, and any community annotations that may have been submitted by other users.
  
  [There is also an API](https://varsome.com/information/varsome-api-info/) you can use to automate the annotation, and [VarSome Pro](https://varsome.com/editions/) that lets you annotate an entire VCF file, but those are both paid services.
  
  ---
  
  **Disclaimer**: I work for the company behind VarSome.
  
  > **Comments:**
  > **username_0**: This looks interesting but *yikes* I don't think it would be much of use in my case since automating the annotation is in my needs. Thanks though.  
  > **username_3**: @Law yeah, the API and/or the Pro version where you can send VCFs would probably be helpful for you, but those aren't free. I thought I'd mention them in case you do have a budget.  
  
  ---
  
  