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.
The major changes in this version were introduced in version 11.7
Please see the version 11.7 Release note for more detailed information.
The following databases have been updated:
Source |
Data Type |
Current (Stable, Q1 '23) |
Next Release (Staging, Q2 '23) |
Comment |
AACT Clinical Trials |
gene |
19-Jan-2023 |
21-Feb-2023 |
|
ACMG classifier |
variant |
11.6.1 |
11.7.2 |
|
AMP classifier |
variant |
11.6.1 |
11.7.2 |
|
ClinVar |
variant |
5-Feb-2023 |
3-Apr-2023 |
|
ClinVar |
region / CNV |
05-Feb-2023 |
03-Apr-2023 |
|
DGI |
gene |
19-Jan-2023 |
21-Feb-2023 |
|
Genomic England PanelAPP |
gene |
20-Jan-2023 |
22-Feb-2023 |
|
GHR |
gene |
19-Jan-2023 |
21-Feb-2023 |
|
gnomAD |
variant |
3.1.1 |
3.1.2 |
|
GWAS |
variant |
20-Jan-2023 |
21-Feb-2023 |
|
Jackson Laboratory CKB |
gene |
24-Jan-2023 |
22-Feb-2023 |
|
Jackson Laboratory CKB |
variant |
24-Jan-2023 |
22-Feb-2023 |
|
LUMC LOVD |
variant |
1-Feb-2023 |
04-Apr-2023 |
|
NIH ClinGen |
variant |
19-Jan-2023 |
21-Feb-2023 |
|
OMIM |
gene |
24-Jan-2023 |
11-Apr-2023 |
|
OMIM |
variant |
24-Jan-2023 |
11-Apr-2023 |
|
PharmGKB |
gene |
20-Oct-2022 |
5-Mar-2023 |
|
PharmGKB |
variant |
19-Sep-2022 |
5-Mar-2023 |
|
Sanger Cosmic |
variant |
v95 |
v97 |
API customers with a valid Cosmic license |
Sanger DECIPHER |
region / CNV |
19-Jan-2023 |
21-Feb-2023 |
|
Saphetor Known Pathogenic |
gene |
06-Feb-2023 |
02-May-2023 |
All clinical classifications from all sources. |
Saphetor Known Pathogenic |
variant |
06-Feb-2023 |
02-May-2023 |
All clinical classifications from all sources. |
Pubmed |
variant |
01-Feb-2023 |
03-May-2023 |
Reminder: all the data structures returned by the VarSome API are documented here.
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
The response changes in this section concern both GET /lookup/{spec_query}/{ref_genome} and POST /lookup/batch/{ref_genome} requests.
Attribute in_silico_thresholds has been removed from the responses of both requests.
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:
Old name |
Renamed to |
NCBI dbVar |
ncbi_dbVar |
TCAG DGV |
tcag_dgv |
Broad ExacCNV |
exacCNV |
NIH GTEx |
nih_gtex |
Sanger DECIPHER |
decipher |
NCBI ClinVar CNVs |
clinvarcnv |
UNIPROT UniProt Regions |
uniprot_regions |
Broad gnomAD structural variants |
gnomad_sv |
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.
The Deafness Variation Database and MaxEntScan database are now present in annotation responses for single variant and batch requests
The pharmgkb attribute in the responses has been modified to include additional information:
The response changes in this section concern both GET /gene/{gene_symbol}/{ref_genome} and POST /genes/batch/{ref_genome} requests.
The pharmgkb attribute in the responses has been modified to include additional information:
The response changes in this section concern GET /cnv/{spec_query}/{ref_genome}
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.