Richard Meyer
CTO
On 10th March 2023 we will be releasing the Q1 API changes for the VarSome API (stable-api.varsome.com).
The Stable API will update version 11.4.5 to version 11.6.1 with data frozen as of the 6th Feb 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 11.5 (version 11.6 is an internal operating system update).
- ACMG
- Improved classification of Mitochondrial variants with inclusions of the MitoTip and MitImpact scores.
- Integration of OMIM into the gene inheritance mode and phenotype matching.
- The classifier now uses MetaRNN instead of BayesDel_addAF.
- The threshold for rule BP1 has been recalibrated for improved specificity.
- Leiden Open Variation Database, LOVD
- A licensed database of approx 310’000 curated variants.
- The LOVD data is available in the API but not yet integrated into the ACMG classifier.
- OMIM
- Improved standardization of phenotype and disease names.
Please see the version 11.5 release note for more detailed information.
Database Updates
The following databases have been updated:
|
Source |
Data Type |
Current (Stable, Q4 '22) |
Next Release (Staging, Q1 '23) |
Comment |
|
AACT Clinical Trials |
gene |
20-Oct-2022 |
19-Jan-2023 |
|
|
ACMG classifier |
variant |
11.4.5 |
11.6.1 |
|
|
AMP classifier |
variant |
11.4.5 |
11.6.1 |
|
|
ClinVar |
variant |
13-Oct-2022 |
5-Feb-2023 |
|
|
CNV classifier |
CNV |
11.4.5 |
11.6.1 |
|
|
dbNSFP |
gene |
4.2 |
4.3 |
|
|
dbNSFP |
variant |
4.2 |
4.3 |
|
|
DGI |
gene |
20-Oct-2022 |
19-Jan-2023 |
|
|
Ensembl Transcripts |
transcript |
107 |
108 |
|
|
Genomic England PanelAPP |
gene |
20-Oct-2022 |
20-Jan-2023 |
|
|
GHR |
gene |
20-Oct-2022 |
19-Jan-2023 |
|
|
GWAS |
variant |
20-Oct-2022 |
20-Jan-2023 |
|
|
LUMC LOVD |
variant |
n/a |
01-Feb-2023 |
New: database of curated variants, see https://www.lovd.nl/ |
|
NIH ClinGen |
variant |
3-Nov-2022 |
19-Jan-2023 |
|
|
OMIM |
gene |
1-Nov-2022 |
24-Jan-2023 |
|
|
OMIM |
variant |
1-Nov-2022 |
24-Jan-2023 |
|
|
Sanger DECIPHER |
region / CNV |
20-Oct-2022 |
19-Jan-2023 |
|
|
Saphetor Known Pathogenic |
gene |
08-Nov-2022 |
03-Feb-2023 |
Gene statistics. |
|
Saphetor Known Pathogenic |
variant |
08-Nov-2022 |
03-Feb-2023 |
All clinical classifications from all sources. |
|
UniProt |
variant |
20-Jun-2022 |
20-Jan-2023 |
|
|
WUSTL CIViC |
gene |
20-Oct-2022 |
21-Nov-2022 |
|
|
WUSTL CIViC |
variant |
20-Oct-2022 |
21-Nov-2022 |
JSON Schema Changes
Reminder: all the data structures returned by the VarSome API are documented here.
dbNSFP 4.3
REVEL Score: similarly to a number of other in-silico scores, instead of a single number in the “revel_score” field, dbNSFP now provides a list of scores, one for each of the Ensembl transcripts referenced.
LOVD
OMIM
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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