Introducing the VarSome API

We are proud to introduce VarSome's high-performance variant annotation Application Programming Interface (API). This powerful API makes it possible to annotate variants using data from over 30 public genomic databases. You can start your project immediately and without incurring the significant overheads of integrating and maintaining all these feeds yourself.

The API has been designed to be as simple as possible to use: a simple REST API is provided, data requests are returned as JSON. This makes it ideal to integrate into Python, R, Perl, Java, or any other programming language.

A full set of documentation is available here, with simple example queries.


A Working Example

We provide a reference API client for Python which demonstrates how to annotate a VCF file. You can simply clone this repository and adapt the code to your own needs.


Annotating Whole Exomes or Genomes

The VarSome API has been designed with performance in mind: in practice it can fully annotate over 600 variants / second over an average internet connection. This is made possible thorugh "batching" requests, as demonstrated in the reference API client: each API request can contain several thousand variants in a single call. A user-configurable allele frequency filter allows you to further increase throughput up to 4x faster: this filter will reject variants whose gnomAD allele frequency is higher than a threshold that you set.


Try it!

Please contact us if you would like to try or evaluate the VarSome API for yourself: we will issue you with an authentication token that will increase your request limits and enable you to batch several variants in a single request.



Saphetor is always trying to innovate and make a positive contribution to human genomics, so do please use the Feedback form (bottom left of the screen) to send us feedback & suggestions as to how we can improve our services.


Plan Free Standard High Volume Dedicated Server
variants per month 100,000 1,000,000 unlimited unlimited
non-variant queries per month 500 5,000 unlimited unlimited
gene queries
option to filter out high frequency variants*
get list of variants in genomic region
ACMG classification
ACMG classification
Price per month $0 $395 contact us contact us

Prices are shown in US dollars. Pricing in Euros, British Pounds and Swiss Francs is also available.

* If the allele frequency filter is enabled, only variants that pass the filter (ie: those below the given frequency or not present in gnomAD genomes) that require annotating will count toward your monthly variants total. High frequency variants will be ignored. This filter is user configurable, and it will likely reduce the actual number of variants that need to be examined by over 95%, thus enabling fast whole exome or genome analysis.

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