Clinvar API help

Question

[Roy]

Hello,

I am a first time user for ClinVar API, and I am trying to find a way to automate some variants I have to an end goal of looking for any clinical significance. I know that I can find the XML I want to parse using the variation ID (example: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=clinvar&rettype=vcv&is_variationid&id=165381&from_esearch=true), but I am trying to automate actually getting the variation ID rather than google each variant I have for it. I have the variant itself (eg. TP53c.455dupC) and transcript ID (eg. NM_001126114.2) for each; will I be able to use either of these in order to obtain the variation ID via a script?

Best, Roy

[vkkodali_ncbi]

If you have the transcript identifier and the HGVS string, you can search ClinVar directly as follows:

$ esearch -db clinvar -query 'NM_000546.6:c.993+409del' | esummary | xtract -pattern DocumentSummary -element Id,accession,title
1259818 VCV001259818    NM_000546.6(TP53):c.993+409del

[GenoMax]

You may want to do this based on gene name search (truncated for space). I think first column is VariationID.

$ esearch -db clinvar -query "TP53 [gene]"| esummary | xtract -pattern DocumentSummary -element Id,accession,variation_name
1298328 VCV001298328    NM_000546.6(TP53):c.376-2A>C
1294447 VCV001294447    Single allele
1292419 VCV001292419    NM_000546.6(TP53):c.-28-112G>A
1288516 VCV001288516    NM_000546.6(TP53):c.993+577A>T
1277877 VCV001277877    NM_000546.6(TP53):c.-28-318_-28-317del
1275830 VCV001275830    NM_000546.6(TP53):c.97-52G>A
1269578 VCV001269578    NM_000546.6(TP53):c.1101-49C>T
1269356 VCV001269356    NM_000546.6(TP53):c.1101-221G>A
1264355 VCV001264355    NM_000546.6(TP53):c.1101-2A>T
1259818 VCV001259818    NM_000546.6(TP53):c.993+409del

Searching with NM_001126114 leads to this same set of results.