... | @@ -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 |
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### Assertion API for v4 ClinGen specifications ( to be published )
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### Assertion API for v4 ClinGen specifications ( to be published )
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#### Introduction
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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 -
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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 -
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[**v4 documentation**](https://genboree.org/gitlab/clingen/cspec/cspec-registry/-/wikis/ACMG-AMP-CAP-ClinGen-v4-Specifications)
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[**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.
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- Route - `/assertion/type/{typeId}` where `typeId` can be either acmg-v3 or acmg-v4.
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- Example `https://genboree.org/cspec/eng/svi/assertion/type/acmg-v4`
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A **payload** contains two required fields - evidence and cspecRuleSetUrl. An example of a payload object is given below:
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>
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> ```plaintext
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> let payload = {
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> cspecRuleSetUrl: 'https://genboree.org/cspec/RuleSet/id/1733626596',
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> // A specific ruleset defined for the v4 specifically.
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> evidence: {
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> 'POP_FRQ_-3': 1,
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> 'CLN_DNV_+4': 1
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> }
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> }
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> ```
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> Examples of how the route works:
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> POST Method
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>
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> ```plaintext
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> const SimpleJsonReq = require( "@brl/brl-gb/client/simple/simpleJsonReq" ).SimpleJsonReq
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> let baseUrl = "https://cspec.genome.network/cspec/eng/svi"
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> let clientOpts = { timeout: 600000 }
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> let jsClient = undefined
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> let resp = undefined
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> jsClient = new SimpleJsonReq( baseUrl, clientOpts )
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> let reqConfig = {
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> serverCertCheck : false,
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> data: payload
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> }
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> resp = await jsClient.doPost('/assertion/type/acmg-v4', reqConfig)
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> console.log(global.brl.insp(global.brl.dot.pick('data', resp.data))) |
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\ No newline at end of file |