openapi.yaml

components:
  schemas:
    ApiAutoACMGSeqVarData:
      properties:
        cds_end:
          description: The CDS end position of the sequence variant
          title: Cds End
          type: integer
        cds_pos:
          description: The CDS position of the sequence variant
          title: Cds Pos
          type: integer
        cds_start:
          description: The CDS start position of the sequence variant
          title: Cds Start
          type: integer
        consequence:
          $ref: '#/components/schemas/AutoACMGConsequence'
          description: The consequence of the sequence variant
        gene_symbol:
          description: The gene symbol of the sequence variant
          title: Gene Symbol
          type: string
        hgnc_id:
          description: The HGNC ID of the sequence variant
          title: Hgnc Id
          type: string
        pHGVS:
          description: The pHGVS notation of the sequence variant
          title: Phgvs
          type: string
        prot_length:
          description: The protein length of the sequence variant
          title: Prot Length
          type: integer
        prot_pos:
          description: The protein position of the sequence variant
          title: Prot Pos
          type: integer
        scores:
          $ref: '#/components/schemas/AutoACMGSeqVarScores'
          description: The scores of the sequence variant
        strand:
          $ref: '#/components/schemas/GenomicStrand'
          description: The strand of the sequence variant
        thresholds:
          $ref: '#/components/schemas/AutoACMGSeqVarTresholds'
          description: The thresholds of the sequence variant
        transcript_id:
          description: The transcript ID of the sequence variant
          title: Transcript Id
          type: string
        transcript_tags:
          description: The transcript tags of the sequence variant
          items:
            type: string
          title: Transcript Tags
          type: array
        tx_pos_utr:
          description: The transcript position in the UTR of the sequence variant
          title: Tx Pos Utr
          type: integer
      required:
      - consequence
      - gene_symbol
      - hgnc_id
      - transcript_id
      - transcript_tags
      - tx_pos_utr
      - cds_pos
      - prot_pos
      - prot_length
      - pHGVS
      - cds_start
      - cds_end
      - strand
      - scores
      - thresholds
      title: ApiAutoACMGSeqVarData
      type: object
    ApiAutoACMGSeqVarResult:
      properties:
        criteria:
          $ref: '#/components/schemas/AutoACMGCriteriaPred'
        data:
          $ref: '#/components/schemas/ApiAutoACMGSeqVarData'
        seqvar:
          $ref: '#/components/schemas/SeqVar'
      required:
      - seqvar
      - data
      - criteria
      title: ApiAutoACMGSeqVarResult
      type: object
    AutoACMGCADD:
      properties:
        ada:
          anyOf:
          - type: number
          - type: 'null'
          title: Ada
        gerp:
          anyOf:
          - type: number
          - type: 'null'
          title: Gerp
        phyloP100:
          anyOf:
          - type: number
          - type: 'null'
          title: Phylop100
        rf:
          anyOf:
          - type: number
          - type: 'null'
          title: Rf
        spliceAI_acceptor_gain:
          anyOf:
          - type: number
          - type: 'null'
          title: Spliceai Acceptor Gain
        spliceAI_acceptor_loss:
          anyOf:
          - type: number
          - type: 'null'
          title: Spliceai Acceptor Loss
        spliceAI_donor_gain:
          anyOf:
          - type: number
          - type: 'null'
          title: Spliceai Donor Gain
        spliceAI_donor_loss:
          anyOf:
          - type: number
          - type: 'null'
          title: Spliceai Donor Loss
      title: AutoACMGCADD
      type: object
    AutoACMGConsequence:
      properties:
        cadd:
          default: ''
          title: Cadd
          type: string
        cadd_consequence:
          default: ''
          title: Cadd Consequence
          type: string
        mehari:
          default: []
          items:
            type: string
          title: Mehari
          type: array
      title: AutoACMGConsequence
      type: object
    AutoACMGCriteria:
      description: Criteria prediction.
      properties:
        description:
          default: ''
          title: Description
          type: string
        name:
          title: Name
          type: string
        prediction:
          $ref: '#/components/schemas/AutoACMGPrediction'
          default: not_set
        strength:
          $ref: '#/components/schemas/AutoACMGStrength'
          default: not_set
        summary:
          default: ''
          title: Summary
          type: string
      required:
      - name
      title: AutoACMGCriteria
      type: object
    AutoACMGCriteriaPred:
      description: ACMG criteria prediction.
      properties:
        ba1:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: BA1
            prediction: not_set
            strength: benign_stand_alone
            summary: ''
        bp1:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: BP1
            prediction: not_set
            strength: benign_supporting
            summary: ''
        bp2:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: BP2
            prediction: not_automated
            strength: benign_supporting
            summary: ''
        bp3:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: BP3
            prediction: not_set
            strength: benign_supporting
            summary: ''
        bp4:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: BP4
            prediction: not_set
            strength: benign_supporting
            summary: ''
        bp5:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: BP5
            prediction: not_automated
            strength: benign_supporting
            summary: ''
        bp6:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: BP6
            prediction: deprecated
            strength: benign_supporting
            summary: ''
        bp7:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: BP7
            prediction: not_set
            strength: benign_supporting
            summary: ''
        bs1:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: BS1
            prediction: not_set
            strength: benign_strong
            summary: ''
        bs2:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: BS2
            prediction: not_set
            strength: benign_strong
            summary: ''
        bs3:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: BS3
            prediction: not_automated
            strength: benign_strong
            summary: ''
        bs4:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: BS4
            prediction: not_automated
            strength: benign_strong
            summary: ''
        pm1:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: PM1
            prediction: not_set
            strength: pathogenic_moderate
            summary: ''
        pm2:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: PM2
            prediction: not_set
            strength: pathogenic_moderate
            summary: ''
        pm3:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: PM3
            prediction: not_automated
            strength: pathogenic_moderate
            summary: ''
        pm4:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: PM4
            prediction: not_set
            strength: pathogenic_moderate
            summary: ''
        pm5:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: PM5
            prediction: not_set
            strength: pathogenic_moderate
            summary: ''
        pm6:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: PM6
            prediction: not_automated
            strength: pathogenic_moderate
            summary: ''
        pp1:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: PP1
            prediction: not_automated
            strength: pathogenic_supporting
            summary: ''
        pp2:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: PP2
            prediction: not_set
            strength: pathogenic_supporting
            summary: ''
        pp3:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: PP3
            prediction: not_set
            strength: pathogenic_supporting
            summary: ''
        pp4:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: PP4
            prediction: not_automated
            strength: pathogenic_supporting
            summary: ''
        pp5:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: PP5
            prediction: deprecated
            strength: pathogenic_supporting
            summary: ''
        ps1:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: PS1
            prediction: not_set
            strength: pathogenic_strong
            summary: ''
        ps2:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: PS2
            prediction: not_automated
            strength: pathogenic_strong
            summary: ''
        ps3:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: PS3
            prediction: not_automated
            strength: pathogenic_strong
            summary: ''
        ps4:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: PS4
            prediction: not_automated
            strength: pathogenic_strong
            summary: ''
        pvs1:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: PVS1
            prediction: not_set
            strength: pathogenic_very_strong
            summary: ''
      title: AutoACMGCriteriaPred
      type: object
    AutoACMGDbnsfp:
      properties:
        alpha_missense:
          anyOf:
          - type: number
          - type: 'null'
          title: Alpha Missense
        bayesDel_noAF:
          anyOf:
          - type: number
          - type: 'null'
          title: Bayesdel Noaf
        fathmm:
          anyOf:
          - type: number
          - type: 'null'
          title: Fathmm
        metaRNN:
          anyOf:
          - type: number
          - type: 'null'
          title: Metarnn
        mutationTaster:
          anyOf:
          - type: number
          - type: 'null'
          title: Mutationtaster
        mutpred:
          anyOf:
          - type: number
          - type: 'null'
          title: Mutpred
        phyloP100:
          anyOf:
          - type: number
          - type: 'null'
          title: Phylop100
        polyphen2:
          anyOf:
          - type: number
          - type: 'null'
          title: Polyphen2
        primateAI:
          anyOf:
          - type: number
          - type: 'null'
          title: Primateai
        provean:
          anyOf:
          - type: number
          - type: 'null'
          title: Provean
        revel:
          anyOf:
          - type: number
          - type: 'null'
          title: Revel
        sift:
          anyOf:
          - type: number
          - type: 'null'
          title: Sift
        vest4:
          anyOf:
          - type: number
          - type: 'null'
          title: Vest4
      title: AutoACMGDbnsfp
      type: object
    AutoACMGDbscsnv:
      properties:
        ada:
          anyOf:
          - type: number
          - type: 'null'
          title: Ada
        rf:
          anyOf:
          - type: number
          - type: 'null'
          title: Rf
      title: AutoACMGDbscsnv
      type: object
    AutoACMGPrediction:
      description: ACMG criteria prediction enumeration.
      enum:
      - not_set
      - applicable
      - not_applicable
      - not_automated
      - deprecated
      - failed
      title: AutoACMGPrediction
      type: string
    AutoACMGSeqVarScores:
      description: ACMG scores.
      properties:
        cadd:
          $ref: '#/components/schemas/AutoACMGCADD'
          default: {}
        dbnsfp:
          $ref: '#/components/schemas/AutoACMGDbnsfp'
          default: {}
        dbscsnv:
          $ref: '#/components/schemas/AutoACMGDbscsnv'
          default: {}
        misZ:
          anyOf:
          - type: number
          - type: 'null'
          title: Misz
      title: AutoACMGSeqVarScores
      type: object
    AutoACMGSeqVarTresholds:
      description: ACMG thresholds.
      properties:
        ada:
          default: 0.957813
          title: Ada
          type: number
        an_min:
          default: 2000
          title: An Min
          type: integer
        ba1_benign:
          default: 0.05
          title: Ba1 Benign
          type: number
        bayesDel_noAF_benign:
          default: -0.476
          title: Bayesdel Noaf Benign
          type: number
        bayesDel_noAF_pathogenic:
          default: 0.521
          title: Bayesdel Noaf Pathogenic
          type: number
        bp7_acceptor:
          default: 2
          title: Bp7 Acceptor
          type: integer
        bp7_donor:
          default: 1
          title: Bp7 Donor
          type: integer
        bs1_benign:
          default: 0.00015
          title: Bs1 Benign
          type: number
        cadd_benign:
          default: 10.0
          title: Cadd Benign
          type: number
        cadd_pathogenic:
          default: 20.0
          title: Cadd Pathogenic
          type: number
        gerp:
          default: 0.0
          title: Gerp
          type: number
        metaRNN_benign:
          default: 0.267
          title: Metarnn Benign
          type: number
        metaRNN_pathogenic:
          default: 0.841
          title: Metarnn Pathogenic
          type: number
        phyloP100:
          default: 3.58
          title: Phylop100
          type: number
        pm1_pathogenic:
          default: 8
          title: Pm1 Pathogenic
          type: number
        pm2_pathogenic:
          default: 0.0001
          title: Pm2 Pathogenic
          type: number
        pp2bp1_benign:
          default: 0.569
          title: Pp2Bp1 Benign
          type: number
        pp2bp1_pathogenic:
          default: 0.808
          title: Pp2Bp1 Pathogenic
          type: number
        pp3bp4_strategy:
          default: default
          title: Pp3Bp4 Strategy
          type: string
        revel_benign:
          default: 0.016
          title: Revel Benign
          type: number
        revel_pathogenic:
          default: 0.773
          title: Revel Pathogenic
          type: number
        rf:
          default: 0.584
          title: Rf
          type: number
        spliceAI_acceptor_gain:
          default: 0.1
          title: Spliceai Acceptor Gain
          type: number
        spliceAI_acceptor_loss:
          default: 0.1
          title: Spliceai Acceptor Loss
          type: number
        spliceAI_donor_gain:
          default: 0.1
          title: Spliceai Donor Gain
          type: number
        spliceAI_donor_loss:
          default: 0.1
          title: Spliceai Donor Loss
          type: number
      title: AutoACMGSeqVarTresholds
      type: object
    AutoACMGStrength:
      description: ACMG criteria strength enumeration.
      enum:
      - not_set
      - pathogenic_very_strong
      - pathogenic_strong
      - pathogenic_moderate
      - pathogenic_supporting
      - benign_stand_alone
      - benign_strong
      - benign_supporting
      title: AutoACMGStrength
      type: string
    AutoACMGStrucVarData:
      properties:
        exons:
          default: []
          items:
            $ref: '#/components/schemas/Exon'
          title: Exons
          type: array
        gene_symbol:
          default: ''
          title: Gene Symbol
          type: string
        hgnc_id:
          default: ''
          title: Hgnc Id
          type: string
        start_cdn:
          default: 0
          title: Start Cdn
          type: integer
        stop_cdn:
          default: 0
          title: Stop Cdn
          type: integer
        strand:
          $ref: '#/components/schemas/GenomicStrand'
          default: not_set
        transcript_id:
          default: ''
          title: Transcript Id
          type: string
        transcript_tags:
          default: []
          items:
            type: string
          title: Transcript Tags
          type: array
      title: AutoACMGStrucVarData
      type: object
    AutoACMGStrucVarPred:
      properties:
        pvs1:
          $ref: '#/components/schemas/AutoACMGCriteria'
          default:
            description: ''
            name: PVS1
            prediction: not_set
            strength: pathogenic_very_strong
            summary: ''
      title: AutoACMGStrucVarPred
      type: object
    AutoACMGStrucVarResult:
      description: Response of the ACMG criteria prediction for structural variants.
      properties:
        criteria:
          $ref: '#/components/schemas/AutoACMGStrucVarPred'
          default:
            pvs1:
              description: ''
              name: PVS1
              prediction: not_set
              strength: pathogenic_very_strong
              summary: ''
        data:
          $ref: '#/components/schemas/AutoACMGStrucVarData'
          default:
            exons: []
            gene_symbol: ''
            hgnc_id: ''
            start_cdn: 0
            stop_cdn: 0
            strand: not_set
            transcript_id: ''
            transcript_tags: []
        strucvar:
          anyOf:
          - $ref: '#/components/schemas/StrucVar'
          - type: 'null'
      title: AutoACMGStrucVarResult
      type: object
    Exon:
      properties:
        altCdsEndI:
          title: Altcdsendi
          type: integer
        altCdsStartI:
          title: Altcdsstarti
          type: integer
        altEndI:
          title: Altendi
          type: integer
        altStartI:
          title: Altstarti
          type: integer
        cigar:
          anyOf:
          - type: string
          - type: 'null'
          title: Cigar
        ord:
          anyOf:
          - type: integer
          - type: 'null'
          title: Ord
      required:
      - altStartI
      - altEndI
      - altCdsStartI
      - altCdsEndI
      title: Exon
      type: object
    GenomeRelease:
      description: Enumeration for allowed genome release values.
      enum:
      - GRCh37
      - GRCh38
      title: GenomeRelease
      type: string
    GenomicStrand:
      description: Genomic strand enumeration.
      enum:
      - plus
      - minus
      - not_set
      title: GenomicStrand
      type: string
    HTTPValidationError:
      properties:
        detail:
          items:
            $ref: '#/components/schemas/ValidationError'
          title: Detail
          type: array
      title: HTTPValidationError
      type: object
    SeqVar:
      properties:
        chrom:
          title: Chrom
          type: string
        delete:
          title: Delete
          type: string
        genome_release:
          $ref: '#/components/schemas/GenomeRelease'
        insert:
          title: Insert
          type: string
        pos:
          title: Pos
          type: integer
        user_repr:
          anyOf:
          - type: string
          - type: 'null'
          title: User Repr
      required:
      - genome_release
      - chrom
      - pos
      - delete
      - insert
      title: SeqVar
      type: object
    SeqVarPredictionResponse:
      properties:
        prediction:
          $ref: '#/components/schemas/ApiAutoACMGSeqVarResult'
          description: The prediction result for the sequence variant
      required:
      - prediction
      title: SeqVarPredictionResponse
      type: object
    StrucVar:
      properties:
        chrom:
          title: Chrom
          type: string
        genome_release:
          $ref: '#/components/schemas/GenomeRelease'
        start:
          title: Start
          type: integer
        stop:
          title: Stop
          type: integer
        sv_type:
          $ref: '#/components/schemas/StrucVarType'
        user_repr:
          anyOf:
          - type: string
          - type: 'null'
          title: User Repr
      required:
      - sv_type
      - genome_release
      - chrom
      - start
      - stop
      title: StrucVar
      type: object
    StrucVarPredictionResponse:
      properties:
        prediction:
          $ref: '#/components/schemas/AutoACMGStrucVarResult'
          description: The prediction result for the structural variant
      required:
      - prediction
      title: StrucVarPredictionResponse
      type: object
    StrucVarType:
      description: Enumeration for structural variant type.
      enum:
      - 1
      - 2
      title: StrucVarType
      type: integer
    ValidationError:
      properties:
        loc:
          items:
            anyOf:
            - type: string
            - type: integer
          title: Location
          type: array
        msg:
          title: Message
          type: string
        type:
          title: Error Type
          type: string
      required:
      - loc
      - msg
      - type
      title: ValidationError
      type: object
    VariantResolveResponse:
      properties:
        resolved_variant:
          anyOf:
          - $ref: '#/components/schemas/SeqVar'
          - $ref: '#/components/schemas/StrucVar'
          description: The resolved variant
          title: Resolved Variant
        variant_type:
          description: The type of the variant (sequence or structural)
          title: Variant Type
          type: string
      required:
      - variant_type
      - resolved_variant
      title: VariantResolveResponse
      type: object
info:
  description: API for AutoACMG
  title: AutoACMG API
  version: 1.0.0
openapi: 3.1.0
paths:
  /api/v1/predict/seqvar:
    get:
      description: "Predict the ACMG classification of a sequence variant.\n\nArgs:\n\
        \    variant_name (str): The name or identifier of the sequence variant.\n\
        \    genome_release (str): The genome release version.\n\nReturns:\n    SeqVarPredictionResponse:\
        \ The predicted ACMG classification."
      operationId: predict_seqvar_api_v1_predict_seqvar_get
      parameters:
      - description: The name or identifier of the sequence variant
        in: query
        name: variant_name
        required: true
        schema:
          description: The name or identifier of the sequence variant
          title: Variant Name
          type: string
      - description: The genome release version
        in: query
        name: genome_release
        required: false
        schema:
          default: GRCh38
          description: The genome release version
          title: Genome Release
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/SeqVarPredictionResponse'
          description: Successful Response
        '422':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
          description: Validation Error
      summary: Predict Seqvar
  /api/v1/predict/strucvar:
    get:
      description: "Predict the ACMG classification of a structural variant.\n\nArgs:\n\
        \    variant_name (str): The name or identifier of the structural variant.\n\
        \    genome_release (str): The genome release version.\n    duplication_tandem\
        \ (bool): The duplication is in tandem and disrupts reading frame and undergoes\
        \ NMD.\n\nReturns:\n    StrucVarPredictionResponse: The predicted ACMG classification."
      operationId: predict_strucvar_api_v1_predict_strucvar_get
      parameters:
      - description: The name or identifier of the structural variant
        in: query
        name: variant_name
        required: true
        schema:
          description: The name or identifier of the structural variant
          title: Variant Name
          type: string
      - description: The genome release version
        in: query
        name: genome_release
        required: false
        schema:
          default: GRCh38
          description: The genome release version
          title: Genome Release
          type: string
      - description: The duplication is in tandem and disrupts reading frame and undergoes
          NMD
        in: query
        name: duplication_tandem
        required: false
        schema:
          default: false
          description: The duplication is in tandem and disrupts reading frame and
            undergoes NMD
          title: Duplication Tandem
          type: boolean
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/StrucVarPredictionResponse'
          description: Successful Response
        '422':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
          description: Validation Error
      summary: Predict Strucvar
  /api/v1/resolve:
    get:
      description: "Resolve a variant to a sequence variant or structural variant.\n\
        \nArgs:\n    variant_name (str): The name or identifier of the variant.\n\
        \    genome_release (str): The genome release version.\n\nReturns:\n    VariantResolveResponse:\
        \ The resolved variant."
      operationId: resolve_variant_api_v1_resolve_get
      parameters:
      - description: The name or identifier of the variant
        in: query
        name: variant_name
        required: true
        schema:
          description: The name or identifier of the variant
          title: Variant Name
          type: string
      - description: The genome release version
        in: query
        name: genome_release
        required: false
        schema:
          default: GRCh38
          description: The genome release version
          title: Genome Release
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/VariantResolveResponse'
          description: Successful Response
        '422':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
          description: Validation Error
      summary: Resolve Variant