Clinical Genomic APIs for Oracle Healthcare Foundation

Retrieve Variant Annotations for a Variant Identifier

get

/ohfapi/cg/v3.3/variants/{id}

This endpoint supports the retrieval of Variant Annotation for a Variant Identifier. It returns assorted Variant Annotation information that include Chromosome, Strand, Allele, Variant Type, Variant Length, Status, Assembly/Alignment Name, Ensembl Version and any Coding Region HGVS notation found. It additionally returns Annotation about any gene the variant falls in, including HUGO Name, Identifier of valid Transcripts, Gene Component Type Regions and other Reference Links

Request

Supported Media Types

application/json
application/xml

Path Parameters

id: integer(int64)

Variant Row ID

Security

basicAuth: basic

Type: basic

Response

Supported Media Types

application/json
application/xml

200 Response

successful operation

Root Schema : VariantAnnotation

Type: object

Show Source

alternateAllele(optional): string

Alternate Allele
assembly(optional): string

Assembly/Alignment Name. For ex.,GRCh38
cancerVariants(optional): string

A link containing href to retrieve Variant Cancer details

Example: {href: '/variants/{variantRecordId}/cancer'}
chromosome(optional): string

Chromosome Name. For ex.,'Y'
diseaseVariants(optional): string

A link containing href to retrieve Variant Disease details

Example: {href: '/variants/{variantRecordId}/diseases'}
endPosition(optional): string

End location of sequence
geneInfo(optional): array geneInfo

List of Variant Genes
identifier(optional): object Identifier

Identifier assigned by a given system
referenceAllele(optional): string

Reference Allele
resourceType(optional): string
startPosition(optional): string

Start location of sequence
status(optional): string

Variant Status
strand(optional): string

Strand Indicator
variantEffect(optional): string

A link containing href to retrieve Variant Effect details

Example: {href: '/variants/{variantRecordId}/variantEffects'}
variantLength(optional): string

Variant Length
variantPrediction(optional): string

A link containing href to retrieve Variant Prediction details

Example: {href: '/variants/{variantRecordId}/variantPredictions'}
variantType(optional): string

Variant Type
variantXref(optional): string

A link containing href to retrieve Variant XRef details

Example: {href: '/variants/{variantRecordId}/variantXRef'}

{
    "type":"object",
    "properties":{
        "resourceType":{
            "type":"string"
        },
        "identifier":{
            "description":"Variant Row ID",
            "$ref":"#/definitions/Identifier"
        },
        "chromosome":{
            "type":"string",
            "description":"Chromosome Name. For ex.,'Y'"
        },
        "startPosition":{
            "type":"string",
            "description":"Start location of sequence"
        },
        "endPosition":{
            "type":"string",
            "description":"End location of sequence"
        },
        "strand":{
            "type":"string",
            "description":"Strand Indicator"
        },
        "referenceAllele":{
            "type":"string",
            "description":"Reference Allele"
        },
        "alternateAllele":{
            "type":"string",
            "description":"Alternate Allele"
        },
        "variantType":{
            "type":"string",
            "description":"Variant Type"
        },
        "variantLength":{
            "type":"string",
            "description":"Variant Length"
        },
        "status":{
            "type":"string",
            "description":"Variant Status"
        },
        "assembly":{
            "type":"string",
            "description":"Assembly/Alignment Name. For ex.,GRCh38"
        },
        "geneInfo":{
            "type":"array",
            "description":"List of Variant Genes",
            "items":{
                "$ref":"#/definitions/VariantAnnotationGene"
            }
        },
        "variantXref":{
            "type":"string",
            "example":"{href: '/variants/{variantRecordId}/variantXRef'}",
            "description":"A link containing href to retrieve Variant XRef details"
        },
        "variantPrediction":{
            "type":"string",
            "example":"{href: '/variants/{variantRecordId}/variantPredictions'}",
            "description":"A link containing href to retrieve Variant Prediction details"
        },
        "variantEffect":{
            "type":"string",
            "example":"{href: '/variants/{variantRecordId}/variantEffects'}",
            "description":"A link containing href to retrieve Variant Effect details"
        },
        "diseaseVariants":{
            "type":"string",
            "example":"{href: '/variants/{variantRecordId}/diseases'}",
            "description":"A link containing href to retrieve Variant Disease details"
        },
        "cancerVariants":{
            "type":"string",
            "example":"{href: '/variants/{variantRecordId}/cancer'}",
            "description":"A link containing href to retrieve Variant Cancer details"
        }
    }
}

Nested Schema : geneInfo

Type: array

List of Variant Genes

Show Source

Array of: object VariantAnnotationGene

{
    "type":"array",
    "description":"List of Variant Genes",
    "items":{
        "$ref":"#/definitions/VariantAnnotationGene"
    }
}

Nested Schema : Identifier

Type: object

Identifier assigned by a given system

Show Source

system(optional): string

System which assigned this identifier
value(optional): string

Identifier value

{
    "type":"object",
    "properties":{
        "system":{
            "type":"string",
            "description":"System which assigned this identifier"
        },
        "value":{
            "type":"string",
            "description":"Identifier value"
        }
    },
    "description":"Identifier assigned by a given system"
}

Nested Schema : VariantAnnotationGene

Type: object

Show Source

gene(optional): object LinkedReference
geneComponents(optional): array geneComponents

List of Gene Components
geneWid(optional): string

Gene Row ID
hgvs(optional): array hgvs

List og HGVS Notations
hugoName(optional): string

Approved HUGO symbol for species loci, including protein coding genes, RNA genes and pseudogenes, e.g. 'SRY', 'DMRT1', 'FOXL2', etc.

{
    "type":"object",
    "properties":{
        "geneWid":{
            "type":"string",
            "description":"Gene Row ID"
        },
        "hugoName":{
            "type":"string",
            "description":"Approved HUGO symbol for species loci, including protein coding genes, RNA genes and pseudogenes, e.g. 'SRY', 'DMRT1', 'FOXL2', etc. "
        },
        "hgvs":{
            "type":"array",
            "description":"List og HGVS Notations",
            "items":{
                "$ref":"#/definitions/Hgvs"
            }
        },
        "geneComponents":{
            "type":"array",
            "description":"List of Gene Components",
            "items":{
                "$ref":"#/definitions/GeneComponent"
            }
        },
        "gene":{
            "example":"{href: '/genes/{GeneRecordId}'}",
            "description":"A link containing href to retrieve Gene details",
            "$ref":"#/definitions/LinkedReference"
        }
    }
}

Nested Schema : LinkedReference

Type: object

Show Source

display(optional): string
reference(optional): string

{
    "type":"object",
    "properties":{
        "reference":{
            "type":"string"
        },
        "display":{
            "type":"string"
        }
    }
}

Nested Schema : geneComponents

Type: array

List of Gene Components

Show Source

Array of: object GeneComponent

{
    "type":"array",
    "description":"List of Gene Components",
    "items":{
        "$ref":"#/definitions/GeneComponent"
    }
}

Nested Schema : hgvs

Type: array

List og HGVS Notations

Show Source

Array of: object Hgvs

{
    "type":"array",
    "description":"List og HGVS Notations",
    "items":{
        "$ref":"#/definitions/Hgvs"
    }
}

Nested Schema : GeneComponent

Type: object

Show Source

ensemblVersion(optional): string

Ensembl Version
transcripts(optional): array transcripts

List of Transcripts

{
    "type":"object",
    "properties":{
        "ensemblVersion":{
            "type":"string",
            "description":"Ensembl Version"
        },
        "transcripts":{
            "type":"array",
            "description":"List of Transcripts",
            "items":{
                "$ref":"#/definitions/Transcript"
            }
        }
    }
}

Nested Schema : transcripts

Type: array

List of Transcripts

Show Source

Array of: object Transcript

{
    "type":"array",
    "description":"List of Transcripts",
    "items":{
        "$ref":"#/definitions/Transcript"
    }
}

Nested Schema : Transcript

Type: object

Show Source

componentTypes(optional): array componentTypes

List of Component Types
transcriptId(optional): string

Transcript ID

{
    "type":"object",
    "properties":{
        "transcriptId":{
            "type":"string",
            "description":"Transcript ID"
        },
        "componentTypes":{
            "type":"array",
            "description":"List of Component Types",
            "items":{
                "type":"string"
            }
        }
    }
}

Nested Schema : componentTypes

Type: array

List of Component Types

Show Source

Array of: string

{
    "type":"array",
    "description":"List of Component Types",
    "items":{
        "type":"string"
    }
}

Nested Schema : Hgvs

Type: object

Show Source

ensemblVersion(optional): string

Ensembl Version
hgvsNotations(optional): array hgvsNotations

List of HGVS Notations

{
    "type":"object",
    "properties":{
        "ensemblVersion":{
            "type":"string",
            "description":"Ensembl Version"
        },
        "hgvsNotations":{
            "type":"array",
            "description":"List of HGVS Notations",
            "items":{
                "type":"string"
            }
        }
    }
}

Nested Schema : hgvsNotations

Type: array

List of HGVS Notations

Show Source

Array of: string

{
    "type":"array",
    "description":"List of HGVS Notations",
    "items":{
        "type":"string"
    }
}

400 Response

Variant Id is not supplied

Examples

The following example submits a GET request.

API URL

http://localhost:7010/ohfapi/cg/v3.3/variants/31486

Example of Response Body

The following example shows the response returned in JSON format.

{
  "resourceType" : "VariantDetails",
  "identifier" : {
    "system" : "ODB",
    "value" : "31486"
  },
  "chromosome" : "1",
  "startPosition" : "1647871",
  "endPosition" : "1647871",
  "strand" : "+",
  "referenceAllele" : "T",
  "alternateAllele" : "C",
  "variantType" : "substitution",
  "variantLength" : "1",
  "status" : "KNOWN",
  "assembly" : "GRCh37",
  "geneInfo" : [ {
    "geneWid" : "137",
    "hugoName" : "CDK11A",
    "hgvs" : [ {
      "ensemblVersion" : "GRCH37.75",
      "hgvsNotations" : [ "ENST00000404249(CDK11A):c.402A>G", "ENST00000358779(CDK11A):c.372A>G", "ENST00000509982(CDK11A):c.402A>G"]
    } ],
    "geneComponents" : [ {
      "ensemblVersion" : "GRCH37.75",
      "transcripts" : [ {
        "transcriptId" : "ENST00000509982",
        "componentTypes" : [ "CDS", "mRNA" ]
      }, {
        "componentTypes" : [ "exon" ]
      }, {
        "transcriptId" : "ENST00000357760",
        "componentTypes" : [ "CDS", "mRNA" ]
      }]
    } ],
    "gene" : {
      "reference" : "/ohfapi/cg/v3.3/genes/137"
    }
  }, {
    "geneWid" : "138",
    "hugoName" : "RP1-283E3.8",
    "geneComponents" : [ {
      "ensemblVersion" : "GRCH37.75",
      "transcripts" : [ {
        "componentTypes" : [ "exon" ]
      }, {
        "transcriptId" : "ENST00000598846",
        "componentTypes" : [ "misc_RNA" ]
      } ]
    } ],
    "gene" : {
      "reference" : "/ohfapi/cg/v3.3/genes/138"
    }
  } ],
  "variantXref" : {
    "reference" : "/ohfapi/cg/v3.3/variants/31486/variantXRef"
  },
  "variantPrediction" : {
    "reference" : "/ohfapi/cg/v3.3/variants/31486/variantPredictions"
  },
  "variantEffect" : {
    "reference" : "/ohfapi/cg/v3.3/variants/31486/variantEffects"
  },
  "diseaseVariants" : {
    "reference" : "/ohfapi/cg/v3.3/variants/31486/diseases"
  },
  "cancerVariants" : {
    "reference" : "/ohfapi/cg/v3.3/variants/31486/cancer"
  }
}