<p>I think the CADD database has this information <a href="https://cadd.gs.washington.edu/download" rel="nofollow noreferrer">https://cadd.gs.washington.edu/download</a>. You want 'All possible SNVs of GRCh38/hg38 incl. all annotations'.</p>

CC BY-SA 4.0
2024-09-26T14:00:46.770Z
2024-09-26T14:06:14.420Z
2024-09-26T14:06:14.420Z
user438383
<p>I'm looking for data which shows the type of SNV variant (at least if the variant synonymous or non-synonymous, and ideally if the variant is in a CDS or not as well) for every variant with respect to the hg38 reference.</p>
<p>For example, a table that shows something along these lines for all variants:</p>
<pre><code>chr1, position 1234, genotype T, reference genotype, not in CDS

chr1, position 1234, genotype A, synonymous variant, not in CDS

chr5, position 1111, genotype G, non-synonymous variant, in CDS
</code></pre>
<p>I don't care which format the data is in or how it is laid out as long as some of this information can be extracted. I don't have a preference between a database of all possible variants (including variation which is not observed in reality) and a database of all variants (polymorphic sites), from, e.g., 1000 Genomes or a similar panel.</p>
<p>I am not looking for deletions, insertions, or CNVs (though it is fine if the dataset has them; I will just exclude them). I'm looking for the annotation (at least if it is synonymous vs. non-synonymous) for every single base-pair variant.</p>

CC BY-SA 4.0
2024-09-27T10:54:18.603Z
When you say for every variant, I assume you mean for "every single-base missense variant", right? No deletions, no insertions, no multi-nt variants. Please clarify that.
terdon
CC BY-SA 4.0
2024-09-27T18:54:49.090Z
@terdon Yes, I'm looking for all single nucleotide variants. It doesn't have to include SVs, CNVs, etc.
BigMistake
<sequence-annotation><database><public-databases><data-download>
Is there a database or file containing the type of variant (e.g., if (non-)synonymous, in exon or not) for all human genomic positions?
# Is there a database or file containing the type of variant (e.g., if (non-)synonymous, in exon or not) for all human genomic positions?

(Asked by: username_0 on 2024-09-25)

I'm looking for data which shows the type of SNV variant (at least if the variant synonymous or non-synonymous, and ideally if the variant is in a CDS or not as well) for every variant with respect to the hg38 reference.
For example, a table that shows something along these lines for all variants:
chr1, position 1234, genotype T, reference genotype, not in CDS

chr1, position 1234, genotype A, synonymous variant, not in CDS

chr5, position 1111, genotype G, non-synonymous variant, in CDS

I don't care which format the data is in or how it is laid out as long as some of this information can be extracted. I don't have a preference between a database of all possible variants (including variation which is not observed in reality) and a database of all variants (polymorphic sites), from, e.g., 1000 Genomes or a similar panel.
I am not looking for deletions, insertions, or CNVs (though it is fine if the dataset has them; I will just exclude them). I'm looking for the annotation (at least if it is synonymous vs. non-synonymous) for every single base-pair variant.

**Tags:** sequence-annotation, database, public-databases, data-download
> **Comments:**
> **username_1**: When you say for every variant, I assume you mean for "every single-base missense variant", right? No deletions, no insertions, no multi-nt variants. Please clarify that.  
> **username_0**: @terdon Yes, I'm looking for all single nucleotide variants. It doesn't have to include SVs, CNVs, etc.  

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## 1 answers

### Answer by username_2 on 2024-09-26. Score: 3

I think the CADD database has this information <https://cadd.gs.washington.edu/download>. You want 'All possible SNVs of GRCh38/hg38 incl. all annotations'.


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