Body: <p>In an <a href="https://pubmed.ncbi.nlm.nih.gov/9768693/" rel="nofollow noreferrer">old article</a>, they gave a table of mutations found in a gene and its positions which points to another <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC326418/pdf/nar00364-0263.pdf" rel="nofollow noreferrer">article</a> containing the FASTA sequence.</p>
  <p>This FASTA is the precursor sequence of the gene. How can I know which transcripts those mutations belong to? And how can I obtain their HGVS format?</p>
  <p>For example, <code>C-7111-G</code> should have an HGVS notation like <code>c.XXXC&gt;G</code>.</p>
  <p><a href="https://i.sstatic.net/UHzyl.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/UHzyl.png" alt="Article" /></a></p>
  <p><a href="https://i.sstatic.net/OuJsU.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/OuJsU.png" alt="FASTA" /></a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-10-07T09:52:09.057Z
Comments.Text: What's the gene? There are tools you can try, but we'd need to know the gene first. And no matter what you do, this will be a manual process since the old FASTA sequence you have is likely inaccurate anyway.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-10-07T15:20:01.417Z
Comments.Text: The gene described in the article is POMC. What I did is the following: first, I copied the same fasta sequence from the old article, then I pinpointed the exact location of the mutations from the table. Second, I copied a couple of unique nucleotides from the left and right of the mutations. Third, I matched those sequences from the actual gene fasta sequence to locate the real nucleotide, and I got its position in the current hg38 build. Then the rest is simple, I searched in the databases what mutations are found in those emplacements.
Comments.UserDisplayName: user324810
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-10-07T15:36:41.727Z
Comments.Text: Yeah, that's probably the best thing you can do. I was going to shamelessly plug the product of the company I work for, https://varsome.com, which is free and can help you translate variant notations, but if all you have is the position relative to an old fasta sequence and don't know the actual transcript, we can't really help much more. You'll be able to get the proper HGVS notation easily though. Same for https://variantvalidator.org/ with which I am not affiliated and which is a great tool for validating HGVS.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-10-07T15:42:57.380Z
Comments.Text: Thank you @terdon. I will check those websites. Cheers!
Comments.UserDisplayName: user324810
Tags: <fasta>
Title: How can I get the HGVS notation of a mutation from a FASTA?
ThreadText: # How can I get the HGVS notation of a mutation from a FASTA?
  
  (Asked by: username_0 on 2022-10-03)
  
  In an [old article](https://pubmed.ncbi.nlm.nih.gov/9768693/), they gave a table of mutations found in a gene and its positions which points to another [article](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC326418/pdf/nar00364-0263.pdf) containing the FASTA sequence.
  
  This FASTA is the precursor sequence of the gene. How can I know which transcripts those mutations belong to? And how can I obtain their HGVS format?
  
  For example, `C-7111-G` should have an HGVS notation like `c.XXXC>G`.
  
  [![Article](https://i.sstatic.net/UHzyl.png)](https://i.sstatic.net/UHzyl.png)
  
  [![FASTA](https://i.sstatic.net/OuJsU.png)](https://i.sstatic.net/OuJsU.png)
  
  **Tags:** fasta
  
  > **Comments:**
  > **username_1**: What's the gene? There are tools you can try, but we'd need to know the gene first. And no matter what you do, this will be a manual process since the old FASTA sequence you have is likely inaccurate anyway.  
  > **username_0**: The gene described in the article is POMC. What I did is the following: first, I copied the same fasta sequence from the old article, then I pinpointed the exact location of the mutations from the table. Second, I copied a couple of unique nucleotides from the left and right of the mutations. Third, I matched those sequences from the actual gene fasta sequence to locate the real nucleotide, and I got its position in the current hg38 build. Then the rest is simple, I searched in the databases what mutations are found in those emplacements.  
  > **username_1**: Yeah, that's probably the best thing you can do. I was going to shamelessly plug the product of the company I work for, https://varsome.com, which is free and can help you translate variant notations, but if all you have is the position relative to an old fasta sequence and don't know the actual transcript, we can't really help much more. You'll be able to get the proper HGVS notation easily though. Same for https://variantvalidator.org/ with which I am not affiliated and which is a great tool for validating HGVS.  
  > **username_0**: Thank you @username_1. I will check those websites. Cheers!  
  
  ---
  
  ## 0 answers
  
  