On December 9th, 2022 we released the Q4 API changes for the VarSome API (stable-api.varsome.com).
The Stable API will update version 11.3.10 to version 11.4.5 with data frozen as of the 11th Nov 2022. This version has been successfully used in production for over a month and includes many improvements to the ACMG classifier in particular.
The most recent version, used by VarSome itself, is always available at api.varsome.com.
Functional Changes
The major changes in this version are:
- ACMG classification updated to use the points-based verdict per ClinGen guidelines
- All in-silico scores have been calibrated per ClinGen guidelines
- MANE Select & MANE Plus transcripts used by ACMG
- New ClinGen database of expert-panel curated variants
Please refer to the following for more detailed information: VarSome Clinical 11.4 Release Note and especially VarSome 11.4 Release Note for the ACMG classifier changes.
Database Updates
The following databases have been updated:
|
Data Source |
Type |
Current (stable) |
Q4 Release |
Comment |
|
Sanger DECIPHER |
Region |
20-Jun-2022 |
20-Oct-2022 |
|
|
Ensembl Transcripts |
Variant |
105 |
107 |
|
|
NCBI ClinVar |
Variant |
06-Jul-2022 |
13-Oct-2022 |
|
|
Weill Cornell PMKB |
Variant |
19-Aug-2021 |
21-Sep-2022 |
|
|
NIH GDC |
Variant |
13-Dec-2021 |
20-Sep-2022 |
|
|
Saphetor Known Pathogenic |
Variant |
03-Aug-2022 |
08-Nov-2022 |
Consolidated classifications from ClinVar, UniProt, MitoMap, & user-linked publications |
|
Pharm GKB |
Variant |
15-Mar-2022 |
19-Sep-2022 |
|
|
ACMG, AMP & CNV classifiers |
Variant |
11.3.10 |
11.4.5 |
See release notes |
|
DGI |
Gene |
15-Jul-2022 |
20-Oct-2022 |
|
|
CGD |
Gene |
15-Mar-2022 |
20-Oct-2022 |
|
|
AACT |
Gene |
15-Jul-2022 |
20-Oct-2022 |
|
|
GHR Genes |
Gene |
13-Jul-2022 |
20-Oct-2022 |
|
|
Genomics England PanelApp |
Gene |
14-Jul-2022 |
20-Oct-2022 |
|
|
FDA Pharmaco genomic biomarkers |
Gene |
16-Sep-2021 |
19-Sep-2022 |
|
|
OMIM |
Gene & Variants |
19-Jul-2022 |
01-Nov-2022 |
New! See JSON schema below |
|
WUSTL CIViC |
Gene & Variants |
13-Jul-2022 |
20-Oct-2022 |
|
|
GWAS |
Variant |
14-Jul-2022 |
20-Oct-2022 |
|
|
NIH ClinGen Variants |
Variant |
n/a |
3-Nov-2022 |
New! See JSON schema below |
JSON Schema Changes
The ACMG_annotation object has changed:
- Additional fields for the points-based verdict:
- pathogenic_score: in points
- benign_score: in points
- total_score: equal to the pathogenic_score minus the benign_score
- clinical_score: the decimal part of this numerical score will have slightly different values; we recommend using the 'verdict' field instead which provides the ACMG class as text
- blosum_score: for missense variants
- transcript_reason: may now say 'MANE select', instead of 'canonical'
The ClinGen curated variants data is now available:
"nih_clingen_variants": [
{
"approval_date": "2022-05-10",
"disease": "juvenile open angle glaucoma",
"evidence_met": [acmg rules as strings]
"evidence_not_met": [acmg rules as strings]
"expert_panel": string
"Guideline": string URL
"mode_of_inheritance": string
"mondo_id": string
"pathogenicity": string
"pub_med_references": array
"published_date": data as string
"repo_link": URL
"retracted": string true/false
"summary": string
"version": date as string
}
]
The OMIM variants data format (was undocumented in 11.3 release):
"omim": [
{
"items": [
{
"alternative_phenotype_names": [String]
"description": String
"mutations": comma separated string
"number": integer,
"omim_id": integer,
"phenotype_name":String",
"references": [list of pub_med_references]
},
… further items
]
"version": data as string,
}
]
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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