Downloading list of known pathogenic non-coding CNVs

Question

[ClkElf]

Dear all, I would like to download known pathogenic non-coding CNVs (enhancers, promoters, TEs etc) including their positions from a database. Could anybody tell me which database I should use & how?

Thank you very much in advance.

Best

Answer 1

[LChart]

The term 'pathogenic' immediately makes me think of ClinVar. The ClinVarMiner resource at UU is pretty browsable for individual conditions; and you can click through the structural variants to the direct ClinVar records:

https://clinvarminer.genetics.utah.edu/variants-by-condition/Autism%20spectrum%20disorder/significance/likely%20pathogenic

https://www.ncbi.nlm.nih.gov/clinvar/RCV000208719/

You can also pull variants directly out of the ClinVar VCF, available here:

https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/