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API · Changes

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Update API authored Apr 26, 2023 by Neethu Shah's avatar Neethu Shah
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...@@ -163,5 +163,40 @@ Assertion API endpoint for computing variant pathogenicity given a set of eviden ...@@ -163,5 +163,40 @@ Assertion API endpoint for computing variant pathogenicity given a set of eviden
### Assertion API for v4 ClinGen specifications ( to be published ) ### Assertion API for v4 ClinGen specifications ( to be published )
#### Introduction
Assertion API endpoint for computing variant pathogenicity given a set of points for each of the criteria codes as defined in the initial draft of v4 guidelines - Technical standards for sequence variant classification v4.0 - ACMG+AMP+CAP+ClinGen. **Note** that the specification codes, point scale, etc. are subject to change. Details can be found here - Assertion API endpoint for computing variant pathogenicity given a set of points for each of the criteria codes as defined in the initial draft of v4 guidelines - Technical standards for sequence variant classification v4.0 - ACMG+AMP+CAP+ClinGen. **Note** that the specification codes, point scale, etc. are subject to change. Details can be found here -
[**v4 documentation**](https://genboree.org/gitlab/clingen/cspec/cspec-registry/-/wikis/ACMG-AMP-CAP-ClinGen-v4-Specifications) [**v4 documentation**](https://genboree.org/gitlab/clingen/cspec/cspec-registry/-/wikis/ACMG-AMP-CAP-ClinGen-v4-Specifications)
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#### POST Request to the engine service _assertion_ route by type.
- Route - `/assertion/type/{typeId}` where `typeId` can be either acmg-v3 or acmg-v4.
- Example `https://genboree.org/cspec/eng/svi/assertion/type/acmg-v4`
A **payload** contains two required fields - evidence and cspecRuleSetUrl. An example of a payload object is given below:
>
> ```plaintext
> let payload = {
> cspecRuleSetUrl: 'https://genboree.org/cspec/RuleSet/id/1733626596',
> // A specific ruleset defined for the v4 specifically.
> evidence: {
> 'POP_FRQ_-3': 1,
> 'CLN_DNV_+4': 1
> }
> }
> ```
> Examples of how the route works:
> POST Method
>
> ```plaintext
> const SimpleJsonReq = require( "@brl/brl-gb/client/simple/simpleJsonReq" ).SimpleJsonReq
> let baseUrl = "https://cspec.genome.network/cspec/eng/svi"
> let clientOpts = { timeout: 600000 }
> let jsClient = undefined
> let resp = undefined
> jsClient = new SimpleJsonReq( baseUrl, clientOpts )
> let reqConfig = {
> serverCertCheck : false,
> data: payload
> }
> resp = await jsClient.doPost('/assertion/type/acmg-v4', reqConfig)
> console.log(global.brl.insp(global.brl.dot.pick('data', resp.data)))
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