// Protocol buffers for types for per-gene impact.

syntax = "proto3";

package annonars.clinvar_data.gene_impact;

import "annonars/clinvar_data/clinvar_public.proto";

// Enumeration with the variant consequence.
enum GeneImpact {
  // unspecified impact
  GENE_IMPACT_UNSPECIFIED = 0;
  // Corresponds to "3_prime_UTR_variant"
  GENE_IMPACT_THREE_PRIME_UTR_VARIANT = 1;
  // Corresponds to "5_prime_UTR_variant"
  GENE_IMPACT_FIVE_PRIME_UTR_VARIANT = 2;
  // Corresponds to "downstream_gene_variant"
  GENE_IMPACT_DOWNSTREAM_TRANSCRIPT_VARIANT = 3;
  // Corresponds to "frameshift_variant"
  GENE_IMPACT_FRAMESHIFT_VARIANT = 4;
  // Corresponds to "inframe_indel"
  GENE_IMPACT_INFRAME_INDEL = 5;
  // Corresponds to "start_lost"
  GENE_IMPACT_START_LOST = 6;
  // Corresponds to "intron_variant"
  GENE_IMPACT_INTRON_VARIANT = 7;
  // Corresponds to "missense_variant"
  GENE_IMPACT_MISSENSE_VARIANT = 8;
  // Corresponds to "non_codnig_transcript_variant"
  GENE_IMPACT_NON_CODING_TRANSCRIPT_VARIANT = 9;
  // Corresponds to "stop_gained"
  GENE_IMPACT_STOP_GAINED = 10;
  // Corresponds to "no_sequence_alteration"
  GENE_IMPACT_NO_SEQUENCE_ALTERATION = 11;
  // Corresponds to "splice_acceptor_variant"
  GENE_IMPACT_SPLICE_ACCEPTOR_VARIANT = 12;
  // Corresponds to "splice_donor_variant"
  GENE_IMPACT_SPLICE_DONOR_VARIANT = 13;
  // Corresponds to "stop_lost"
  GENE_IMPACT_STOP_LOST = 14;
  // Corresponds to "synonymous_variant"
  GENE_IMPACT_SYNONYMOUS_VARIANT = 15;
  // Corresponds to "upstream_gene_variant"
  GENE_IMPACT_UPSTREAM_TRANSCRIPT_VARIANT = 16;
}


// Enumeration for ACMG clinical significance.
enum ClinicalSignificance {
  // unspecified clinical significance
  CLINICAL_SIGNIFICANCE_UNSPECIFIED = 0;
  // Corresponds to "Benign"
  CLINICAL_SIGNIFICANCE_BENIGN = 1;
  // Corresponds to "Likely benign"
  CLINICAL_SIGNIFICANCE_LIKELY_BENIGN = 2;
  // Corresponds to "Uncertain significance"
  CLINICAL_SIGNIFICANCE_UNCERTAIN_SIGNIFICANCE = 3;
  // Corresponds to "Likely pathogenic"
  CLINICAL_SIGNIFICANCE_LIKELY_PATHOGENIC = 4;
  // Corresponds to "Pathogenic"
  CLINICAL_SIGNIFICANCE_PATHOGENIC = 5;
  // Corresponds to "not provided"
  CLINICAL_SIGNIFICANCE_NOT_PROVIDED = 6;
  // Corresponds to "other"
  CLINICAL_SIGNIFICANCE_OTHER = 7;
}


// Entry for storing counts of `GeneImpact` and `ClinicalSignificance`.
message GeneImpactCounts {
  // Stores the counts for a gene impact.
  message ImpactCounts {
    // The gene impact.
    GeneImpact gene_impact = 1;
    // The counts for the benign impact.
    uint32 count_benign = 2;
    // The counts for the likely benign impact.
    uint32 count_likely_benign = 3;
    // The counts for the uncertain significance impact.
    uint32 count_uncertain_significance = 4;
    // The counts for the likely pathogenic impact.
    uint32 count_likely_pathogenic = 5;
    // The counts for the pathogenic impact.
    uint32 count_pathogenic = 6;
  }

  // The gene HGNC ID.
  string hgnc_id = 1;
  // The impact counts.
  repeated ImpactCounts impact_counts = 2;
}