feat: new acmg criteria structure

frontend/src/components/ACMG/acmgInterfaces.ts

@@ -0,0 +1,373 @@
+interface CriteriaDescType {
+  id: string
+  label: string
+  hint: string
+}
+
+const CriteriaDefinitions: Record<string, CriteriaDescType> = {
+  pvs1: {
+    id: 'pvs1',
+    label: 'PVS1',
+    hint: 'null variant'
+  },
+  ps1: {
+    id: 'ps1',
+    label: 'PS1',
+    hint: 'same amino acid change'
+  },
+  ps2: {
+    id: 'ps2',
+    label: 'PS2',
+    hint: 'de novo (both maternity and paternity confirmed)'
+  },
+  ps3: {
+    id: 'ps3',
+    label: 'PS3',
+    hint: 'well-established in vitro or in vivo functional studies'
+  },
+  ps4: {
+    id: 'ps4',
+    label: 'PS4',
+    hint: 'prevalence in disease controls'
+  },
+  pm1: {
+    id: 'pm1',
+    label: 'PM1',
+    hint: 'variant in hotspot (missense)'
+  },
+  pm2: {
+    id: 'pm2',
+    label: 'PM2',
+    hint: 'absent from controls (or at extremely low frequency if recessive)'
+  },
+  pm3: {
+    id: 'pm3',
+    label: 'PM3',
+    hint: 'AR: trans with known pathogenic'
+  },
+  pm4: {
+    id: 'pm4',
+    label: 'PM4',
+    hint: 'protein length change'
+  },
+  pm5: {
+    id: 'pm5',
+    label: 'PM5',
+    hint: 'literature: AA exchange same pos'
+  },
+  pm6: {
+    id: 'pm6',
+    label: 'PM6',
+    hint: 'assumed de novo'
+  },
+  pp1: {
+    id: 'pp1',
+    label: 'PP1',
+    hint: 'cosegregates in family'
+  },
+  pp2: {
+    id: 'pp2',
+    label: 'PP2',
+    hint: 'few missense in gene'
+  },
+  pp3: {
+    id: 'pp3',
+    label: 'PP3',
+    hint: 'predicted pathogenic'
+  },
+  pp4: {
+    id: 'pp4',
+    label: 'PP4',
+    hint: 'phenotype/pedigree match gene'
+  },
+  pp5: {
+    id: 'pp5',
+    label: 'PP5',
+    hint: 'reliable source: pathogenic'
+  },
+  ba1: {
+    id: 'ba1',
+    label: 'BA1',
+    hint: 'AF > 5% in ExAC, 1000G, or ESP'
+  },
+  bs1: {
+    id: 'bs1',
+    label: 'BS1',
+    hint: 'disease: allele freq. too high'
+  },
+  bs2: {
+    id: 'bs2',
+    label: 'BS2',
+    hint: 'observed in healthy individual'
+  },
+  bs3: {
+    id: 'bs3',
+    label: 'BS3',
+    hint: 'functional studies: benign'
+  },
+  bs4: {
+    id: 'bs4',
+    label: 'BS4',
+    hint: 'lack of segregation'
+  },
+  bp1: {
+    id: 'bp1',
+    label: 'BP1',
+    hint: 'missense in gene with truncating'
+  },
+  bp2: {
+    id: 'bp2',
+    label: 'BP2',
+    hint: 'other variant is causative'
+  },
+  bp3: {
+    id: 'bp3',
+    label: 'BP3',
+    hint: 'in-frame indel'
+  },
+  bp4: {
+    id: 'bp4',
+    label: 'BP4',
+    hint: 'prediction: benign'
+  },
+  bp5: {
+    id: 'bp5',
+    label: 'BP5',
+    hint: 'different gene in other case'
+  },
+  bp6: {
+    id: 'bp6',
+    label: 'BP6',
+    hint: 'reputable source: benign'
+  },
+  bp7: {
+    id: 'bp7',
+    label: 'BP7',
+    hint: 'silent, no splicing/conservation'
+  }
+}
+
+enum AcmgEvidenceLevel {
+  PVS = 8,
+  PS = 4,
+  PM = 2,
+  PP = 1,
+  BA = -8,
+  BS = -4,
+  BP = -2
+}
+
+interface CriteriaStateType {
+  id: string
+  active: boolean
+  evidence: AcmgEvidenceLevel
+  description: string
+}
+
+const CriteriaState: Record<string, CriteriaStateType> = {
+  pvs1: {
+    id: 'pvs1',
+    active: false,
+    evidence: AcmgEvidenceLevel.PVS,
+    description:
+      'Null variant (nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon, single or multi-exon deletion) in a gene where LOF is a known mechanism of disease'
+  },
+  ps1: {
+    id: 'ps1',
+    active: false,
+    evidence: AcmgEvidenceLevel.PS,
+    description:
+      'Same amino acid change as a previously established pathogenic variant regardless of nucleotide change'
+  },
+  ps2: {
+    id: 'ps2',
+    active: false,
+    evidence: AcmgEvidenceLevel.PS,
+    description:
+      'De novo (both maternity and paternity confirmed) in a patient with the disease and no family history'
+  },
+  ps3: {
+    id: 'ps3',
+    active: false,
+    evidence: AcmgEvidenceLevel.PS,
+    description:
+      'Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product'
+  },
+  ps4: {
+    id: 'ps4',
+    active: false,
+    evidence: AcmgEvidenceLevel.PS,
+    description:
+      'The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls'
+  },
+  pm1: {
+    id: 'pm1',
+    active: false,
+    evidence: AcmgEvidenceLevel.PM,
+    description:
+      'Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation'
+  },
+  pm2: {
+    id: 'pm2',
+    active: false,
+    evidence: AcmgEvidenceLevel.PM,
+    description:
+      'Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium'
+  },
+  pm3: {
+    id: 'pm3',
+    active: false,
+    evidence: AcmgEvidenceLevel.PM,
+    description: 'For recessive disorders, detected in trans with a pathogenic variant'
+  },
+  pm4: {
+    id: 'pm4',
+    active: false,
+    evidence: AcmgEvidenceLevel.PM,
+    description:
+      'Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants'
+  },
+  pm5: {
+    id: 'pm5',
+    active: false,
+    evidence: AcmgEvidenceLevel.PM,
+    description:
+      'Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before'
+  },
+  pm6: {
+    id: 'pm6',
+    active: false,
+    evidence: AcmgEvidenceLevel.PM,
+    description: 'Assumed de novo, but without confirmation of paternity and maternity'
+  },
+  pp1: {
+    id: 'pp1',
+    active: false,
+    evidence: AcmgEvidenceLevel.PP,
+    description:
+      'Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease'
+  },
+  pp2: {
+    id: 'pp2',
+    active: false,
+    evidence: AcmgEvidenceLevel.PP,
+    description:
+      'Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease'
+  },
+  pp3: {
+    id: 'pp3',
+    active: false,
+    evidence: AcmgEvidenceLevel.PP,
+    description:
+      'Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.)'
+  },
+  pp4: {
+    id: 'pp4',
+    active: false,
+    evidence: AcmgEvidenceLevel.PP,
+    description:
+      "Patient's phenotype or family history is highly specific for a disease with a single genetic etiology"
+  },
+  pp5: {
+    id: 'pp5',
+    active: false,
+    evidence: AcmgEvidenceLevel.PP,
+    description:
+      'Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratoryto perform an independent evaluation'
+  },
+  ba1: {
+    id: 'ba1',
+    active: false,
+    evidence: AcmgEvidenceLevel.BA,
+    description:
+      'Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium'
+  },
+  bs1: {
+    id: 'bs1',
+    active: false,
+    evidence: AcmgEvidenceLevel.BS,
+    description: 'Allele frequency is greater than expected for disorder'
+  },
+  bs2: {
+    id: 'bs2',
+    active: false,
+    evidence: AcmgEvidenceLevel.BS,
+    description:
+      'Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age'
+  },
+  bs3: {
+    id: 'bs3',
+    active: false,
+    evidence: AcmgEvidenceLevel.BS,
+    description:
+      'Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing'
+  },
+  bs4: {
+    id: 'bs4',
+    active: false,
+    evidence: AcmgEvidenceLevel.BS,
+    description: 'Lack of segregation in affected members of a family'
+  },
+  bp1: {
+    id: 'bp1',
+    active: false,
+    evidence: AcmgEvidenceLevel.BP,
+    description:
+      'Missense variant in a gene for which primarily truncating variants are known to cause disease'
+  },
+  bp2: {
+    id: 'bp2',
+    active: false,
+    evidence: AcmgEvidenceLevel.BP,
+    description:
+      'Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern'
+  },
+  bp3: {
+    id: 'bp3',
+    active: false,
+    evidence: AcmgEvidenceLevel.BP,
+    description: 'In-frame deletions/insertions in a repetitive region without a known function'
+  },
+  bp4: {
+    id: 'bp4',
+    active: false,
+    evidence: AcmgEvidenceLevel.BP,
+    description:
+      'Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary,splicing impact, etc.)'
+  },
+  bp5: {
+    id: 'bp5',
+    active: false,
+    evidence: AcmgEvidenceLevel.BP,
+    description: 'Variant found in a case with an alternate molecular basis for disease'
+  },
+  bp6: {
+    id: 'bp6',
+    active: false,
+    evidence: AcmgEvidenceLevel.BP,
+    description:
+      'Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation'
+  },
+  bp7: {
+    id: 'bp7',
+    active: false,
+    evidence: AcmgEvidenceLevel.BP,
+    description:
+      'A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved'
+  }
+}
+
+const ACMGRanking = {
+  default: { ...CriteriaState },
+  interVar: { ...CriteriaState },
+  userSelected: { ...CriteriaState }
+}
+
+export {
+  type CriteriaDescType,
+  CriteriaDefinitions,
+  AcmgEvidenceLevel,
+  type CriteriaStateType,
+  CriteriaState,
+  ACMGRanking
+}