{
   "$schema": "https://json-schema.org/draft/2020-12/schema",
   "title": "Variant Annotation Format",
   "description": "The variant annotation/interpretation format stores associations of variation with annotations/intreptations.",
   "type": "object",
   "properties": {
      "_version": {
         "$ref": "../../core.json#/definitions/Version"
      },
      "findings": {
         "items": {
            "$ref": "#/definitions/Interpretation"
         },
         "minItems": 1,
         "maxItems": 10,
         "type": "array"
      },
      "references": {
         "type": "array",
         "items": {
            "$ref": "../../structs.json#/definitions/Reference"
         }
      }
   },
   "definitions": {
      "Interpretation": {
         "type": "object",
         "properties": {
            "classification": {
               "type": "object",
               "properties": {
                  "scheme": {
                     "type": "string",
                     "enum": [
                        "ACMG"
                     ]
                  },
                  "value": {
                     "type": "string",
                     "anyOf": [
                        {
                           "$ref": "../../core.json#/definitions/ACMGClassification"
                        },
                        {
                           "const": "NEGATIVE"
                        }
                     ]
                  }
               }
            },
            "condition": {
               "type": [
                  "string",
                  "null"
               ],
               "example": [
                  "breast_cancer"
               ]
            },
            "evidence": {
               "type": "object",
               "properties": {
                  "summary": {
                     "type": "string",
                     "description": "Interpretation summary",
                     "example": "lorem ipsum"
                  }
               }
            },
            "gene_symbol": {
               "type": "string",
               "description": "Gene symbol",
               "example": "PEX1"
            },
            "event": {
               "title": "Variant Event",
               "type": [
                  "string",
                  "null"
               ]
            },
            "inheritance": {
               "description": "Who the variant is inherited from",
               "$ref": "../../core.json#/definitions/VariantInheritance"
            },
            "zygosity": {
               "description": "Zygosity of the variant in the individual",
               "$ref": "../../core.json#/definitions/Zygosity"
            },
            "variation": {
               "$ref": "../../structs.json#/definitions/RareDiseaseVariation"
            },
            "gene_info": {
               "type": "string",
               "description": "Information text about the gene",
               "example": "This gene encodes a member of the AAA ATPase family, a large group of ATPases associated with diverse cellular activities. This protein is cytoplasmic but is often anchored to a peroxisomal membrane where it forms a heteromeric complex and plays a role in the import of proteins into peroxisomes and peroxisome biogenesis. Mutations in this gene have been associated with complementation group 1 peroxisomal disorders such as neonatal adrenoleukodystrophy, infantile Refsum disease, and Zellweger syndrome. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2013]"
            },
            "variant_description": {
               "type": "string",
               "description": "Long text description of the variant",
               "example": "Non-canonical splice variant c.1359+601A>G located in intron 6 of the PEX1 gene is predicted by computational tools to create a cryptic splice site. This could lead to disrupted production of the PEX1 gene product. This variant is absent from large population databases, including gnomAD. This variant was not found in ClinVar. This variant has not been reported in the literature. Based on the evidence above and according to the ACMG/AMP variant interpretation guidelines, this variant has been classified as a variant of uncertain significance. Additional information is needed to resolve the significance of this variant."
            },
            "mode_of_inheritance": {
               "description": "Mode of inheritance of the condition",
               "$ref": "../../core.json#/definitions/Inheritance"
            }
         }
      }
   }
}