| ... | ... | @@ -14,7 +14,8 @@ Assertion API endpoint for computing variant pathogenicity given a set of eviden |
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> ```plaintext
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> let payload = {
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> cspecRuleSetUrl: 'https://cspec.genome.network/cspec/RuleSet/id/643243101',
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> cspecRuleSetUrl: 'https://cspec.genome.network/cspec/RuleSet/id/643243101',
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> // A specific ruleset defined by DICER1 and miRNA-Processing Gene Variant Curation Expert Panel - https://clinicalgenome.org/affiliation/50050
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> evidence: {
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> 'Pathogenic.Moderate': 2,
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> 'Pathogenic.Strong': 1,
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| ... | ... | @@ -23,118 +24,120 @@ Assertion API endpoint for computing variant pathogenicity given a set of eviden |
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> }
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> }
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> ```
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>
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> Example of how the route works:
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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.doGet('/assertion', reqConfig)
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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.doGet('/assertion', reqConfig)
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> console.log(global.brl.insp(global.brl.dot.pick('data', resp.data)))
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{
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comment: 'Two assertions: Pathogenic and Likely Pathogenic were made. In such case ' +
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'the final call is the highest strength call, hence the allele is ' +
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'Pathogenic',
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finalCall: 'Pathogenic',
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rules: [
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{
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conditions: [
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{
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applicableCriteriaCodes: [
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'PVS1',
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'PS2_Very Strong'
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],
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condition: '==1',
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label: 'Rule1, Condition1',
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partitionPath: 'Pathogenic.Very Strong'
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},
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{
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applicableCriteriaCodes: [
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'PS1',
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'PS2',
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'PS3',
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'PS4',
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'PP1_Strong'
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],
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condition: '>=1',
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label: 'Rule1, Condition2',
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partitionPath: 'Pathogenic.Strong'
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}
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],
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inference: 'Pathogenic',
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rule: 'Rule1'
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},
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{
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conditions: [
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{
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applicableCriteriaCodes: [
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'PVS1',
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'PS2_Very Strong'
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],
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condition: '==1',
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label: 'Rule2, Condition1',
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partitionPath: 'Pathogenic.Very Strong'
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},
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{
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applicableCriteriaCodes: [
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'PS2_Moderate',
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'PS3_Moderate',
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'PS4_Moderate',
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'PM1',
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'PM4',
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'PM5',
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'PP1_Moderate'
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],
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condition: '>=2',
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label: 'Rule2, Condition2',
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partitionPath: 'Pathogenic.Moderate'
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}
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],
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inference: 'Pathogenic',
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rule: 'Rule2'
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},
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{
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conditions: [
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{
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applicableCriteriaCodes: [
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'PS1',
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'PS2',
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'PS3',
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'PS4',
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'PP1_Strong'
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],
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condition: '==1',
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label: 'Rule20, Condition1',
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partitionPath: 'Pathogenic.Strong'
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},
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{
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applicableCriteriaCodes: [
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'PS2_Moderate',
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'PS3_Moderate',
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'PS4_Moderate',
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'PM1',
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'PM4',
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'PM5',
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'PP1_Moderate'
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],
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condition: '==2',
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label: 'Rule20, Condition2',
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partitionPath: 'Pathogenic.Moderate'
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}
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],
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inference: 'Likely Pathogenic',
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rule: 'Rule20'
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}
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],
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statusObj: {
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name: 'assertion computed',
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status: 'ok'
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}
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} |
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\ No newline at end of file |
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> {
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> comment: 'Two assertions: Pathogenic and Likely Pathogenic were made. In such case ' +
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> 'the final call is the highest strength call, hence the allele is ' +
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> 'Pathogenic',
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> finalCall: 'Pathogenic',
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> rules: [
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> {
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> conditions: [
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> {
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> applicableCriteriaCodes: [
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> 'PVS1',
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> 'PS2_Very Strong'
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> ],
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> condition: '==1',
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> label: 'Rule1, Condition1',
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> partitionPath: 'Pathogenic.Very Strong'
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> },
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> {
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> applicableCriteriaCodes: [
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> 'PS1',
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> 'PS2',
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> 'PS3',
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> 'PS4',
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> 'PP1_Strong'
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> ],
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> condition: '>=1',
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> label: 'Rule1, Condition2',
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> partitionPath: 'Pathogenic.Strong'
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> }
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> ],
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> inference: 'Pathogenic',
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> rule: 'Rule1'
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> },
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> {
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> conditions: [
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> {
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> applicableCriteriaCodes: [
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> 'PVS1',
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> 'PS2_Very Strong'
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> ],
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> condition: '==1',
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> label: 'Rule2, Condition1',
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> partitionPath: 'Pathogenic.Very Strong'
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> },
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> {
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> applicableCriteriaCodes: [
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> 'PS2_Moderate',
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> 'PS3_Moderate',
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> 'PS4_Moderate',
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> 'PM1',
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> 'PM4',
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> 'PM5',
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> 'PP1_Moderate'
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> ],
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> condition: '>=2',
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> label: 'Rule2, Condition2',
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> partitionPath: 'Pathogenic.Moderate'
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> }
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> ],
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> inference: 'Pathogenic',
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> rule: 'Rule2'
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> },
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> {
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> conditions: [
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> {
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> applicableCriteriaCodes: [
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> 'PS1',
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> 'PS2',
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> 'PS3',
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> 'PS4',
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> 'PP1_Strong'
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> ],
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> condition: '==1',
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> label: 'Rule20, Condition1',
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> partitionPath: 'Pathogenic.Strong'
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> },
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> {
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> applicableCriteriaCodes: [
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> 'PS2_Moderate',
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> 'PS3_Moderate',
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> 'PS4_Moderate',
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> 'PM1',
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> 'PM4',
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> 'PM5',
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> 'PP1_Moderate'
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> ],
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> condition: '==2',
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> label: 'Rule20, Condition2',
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> partitionPath: 'Pathogenic.Moderate'
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> }
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> ],
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> inference: 'Likely Pathogenic',
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> rule: 'Rule20'
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> }
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> ],
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> statusObj: {
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> name: 'assertion computed',
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> status: 'ok'
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> }
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> }
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> ``` |
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\ No newline at end of file |
