On 9th June 2023 we will be releasing the Q2 API changes for the VarSome API (stable-api.varsome.com).

The Stable API will update version 11.6.1 to version 11.7.2  with data frozen as of the 12th May 2023. This version has been successfully used in production for over a month.

The most recent version, used by VarSome itself, is always available at api.varsome.com.

Functional Changes

The major changes in this version were introduced in version 11.7

• Overall improvements:
  • Various in-silico predictors improvements
  • Extension of HGVS notation supported by VarSome to include single amino acid deletions and duplications within the same exon
  • Information from the Deafness Variation Database from the University of Iowa is now available in VarSome
• Germline classification:
  • Integration of LOVD evidence as a new source available to Premium users
  • Modifications in the way we filter gnomAD improvements
  • Further inclusion of ClinGen recommendations for mitochondrial variants
  • New in-silico pathogenicity predictor for splice sites, MaxEntScan
• Somatic classification:
  • The somatic classifier no longer uses Cosmic
    
    

Please see the version 11.7 Release note for more detailed information.

Database Updates

The following databases have been updated:

JSON Schema Changes

Reminder: all the data structures returned by the VarSome API are documented here.

Variant Annotation Schema Changes  

Body modifications

The following request:

POST /lookup/batch/{ref_genome} accepts now an additional parameter, variant_specs

The new parameter is optional and should be ignored by VarSome API users, as it is intended for specific Saphetor installations

Response modifications

The response changes in this section concern both GET /lookup/{spec_query}/{ref_genome} and POST /lookup/batch/{ref_genome} requests.

Attribute removals

Attribute in_silico_thresholds has been removed from the responses of both requests.

Region Database schema changes

Variant annotation responses under the regions key follow now a specific schema per source database, as is described below.

Region database json keys have also been changed for uniformity:

The regions part of json responses now is standardized as follows in single variant  and batch requests:

The detailed response schema per source can be found in the online documentation.

New Databases 

The Deafness Variation Database and MaxEntScan database are now present in annotation responses for single variant and batch requests

Other Attribute modifications

The pharmgkb attribute in the responses has been modified to include additional information:

Gene Annotation Schema Changes 

Response modifications

The response changes in this section concern both GET /gene/{gene_symbol}/{ref_genome} and POST /genes/batch/{ref_genome} requests.

Attribute modifications

The pharmgkb attribute in the responses has been modified to include additional information:

CNV Annotation Schema Changes 

Response modifications

The response changes in this section concern GET /cnv/{spec_query}/{ref_genome} 

Region Database schema changes

CNV annotation responses under the regions key follow now a specific schema per source database, as described in the Variant Annotation Schema Changes section of this document.

Further Information and Support

An overview of the VarSome API is available here with more detailed information here.

Please contact us at the usual address support@varsome.com should you require any additional information or run into any major issues. As ever we look forward to your feedback and suggestions to improve our platform.