On September 9th, 2022 the Q3 API changes for the VarSome API (stable-api.varsome.com) were released.
The Stable API will update version 11.2.12 to version 11.3.10 with data frozen as of the 3rd August 2022. This version has been successfully used in production for two months and includes many improvements.
The most recent version, used by VarSome itself, is always available at api.varsome.com.
Functional Changes
The major changes in this version are:
- New gene databases:
- OMIM database linking genes to phenotypes and modes of inheritance
- The Gene Curation Coalition: GEN CC
- ClinGen Gene-Disease Validity
- EBI Gene 2 Phenotype
- New variant Database of Curated Mutations (DoCM)
- New EVE pathogenicity score for missense variants.
- Improvements to the automated ACMG, AMP and CNV classifiers.
Of particular note: ACMG rule PVS1 now implements the recommendations for NMD, and furthermore will not trigger for oncogenes when in somatic mode.
Please refer to the following for more detailed information: VarSome 11.3 Release Notes.
Database Updates
The following databases have been updated, the JSON schema changes below should have minimal impact:
|
Databases |
Current |
Q3 Release |
Comment |
|---|---|---|---|
|
ACMG, AMP & CNV classifiers |
11.2.12 |
11.3.10 |
See VarSome 11.3 Release Notes for full details. |
|
EVE |
n/a |
07-Jun-2022 |
New: in-silico prediction score |
|
EBI Gene to Phenotype |
n/a |
07-Jun-2022 |
New: gene/disease associations. JSON key “ebi_gene_2_phenotype” |
|
GEN CC |
n/a |
07-Jun-2022 |
New: gene/disease associations |
|
OMIM |
n/a |
19-Jul-2022 |
New: licensed gene/phenotype associations with modes of inheritance + information on specific variants. JSON key “omim” |
|
NIH ClinGen Disease Validity |
n/a |
07-Jun-2022 |
New: gene/disease associations. JSON key “nih_clin_gen_disease_validity” |
|
WUSTL DoCM |
n/a |
07-Jun-2022 |
New: database of cancer mutations. JSON key “wustl_docm” |
|
Saphetor “Known Pathogenic” variants |
3 Aug 2022 |
Database of all reported germline variants from ClinVar, MitoMap, UniProt, and curated publications. |
|
|
NCBI ClinVar CNVs |
14-Mar-2022 |
06-Jul-2022 |
|
|
Sanger DECIPHER |
17-Apr-2022 |
20-Jun-2022 |
|
|
NCBI Clinvar |
14-Mar-2022 |
06-Jul-2022 |
|
|
UNIPROT variants |
15-Mar-2022 |
20-Jun-2022 |
|
|
UNIPROT Regions |
15-Mar-2022 |
20-Jun-2022 |
|
|
cBIO Portal |
23-Mar-2022 |
21-Jun-2022 |
|
|
JAX CKB |
18-Apr-2022 |
18-Jul-2022 |
Not available in the API, can only be licensed to users of VarSome Clinical. |
|
DGI |
09-Sep-2021 |
15-Jul-2022 |
|
|
WUSTL CIViC |
17-Apr-2022 |
13-Jul-2022 |
|
|
AACT |
17-Apr-2022 |
15-Jul-2022 |
|
|
GHR Genes |
15-Mar-2022 |
13-Jul-2022 |
|
|
Genomics England PanelAPP |
17-Apr-2022 |
14-Jul-2022 |
|
|
ClinGen Gene |
23-Feb-2022 |
07-Jun-2022 |
|
|
GWAS |
17-Apr-2022 |
14-Jul-2022 |
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.
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