REST API for Oracle Healthcare Translational Research

Retrieve Variant Annotations for a Variant Identifier

get

/HSDataService-web/api/3.2.0/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: Type: integer (int64)

Required: true

Variant Row ID

Response

Supported Media Types

application/json
application/xml

200 Response

successful operation

Body

Root Schema : VariantAnnotation

Type: object

Properties

alternateAllele: Type: string

Alternate Allele
assembly: Type: string

Assembly/Alignment Name. For ex.,GRCh38
cancerVariants: Type: string

A link containing href to retrieve Variant Cancer details

Example: {href: '/variants/{variantRecordId}/cancer'}
chromosome: Type: string

Chromosome Name. For ex.,'Y'
diseaseVariants: Type: string

A link containing href to retrieve Variant Disease details

Example: {href: '/variants/{variantRecordId}/diseases'}
endPosition: Type: string

End location of sequence
geneInfo: Type: array geneInfo

List of Variant Genes
identifier: Type: object Identifier

Identifier assigned by a given system
referenceAllele: Type: string

Reference Allele
resourceType: Type: string
startPosition: Type: string

Start location of sequence
status: Type: string

Variant Status
strand: Type: string

Strand Indicator
variantEffect: Type: string

A link containing href to retrieve Variant Effect details

Example: {href: '/variants/{variantRecordId}/variantEffects'}
variantLength: Type: string

Variant Length
variantPrediction: Type: string

A link containing href to retrieve Variant Prediction details

Example: {href: '/variants/{variantRecordId}/variantPredictions'}
variantType: Type: string

Variant Type
variantXref: Type: string

A link containing href to retrieve Variant XRef details

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

Nested Schema : geneInfo

Type: array

List of Variant Genes

Items

Type: object VariantAnnotationGene

Nested Schema : Identifier

Type: object

Identifier assigned by a given system

Properties

system: Type: string

System which assigned this identifier
value: Type: string

Identifier value

Nested Schema : VariantAnnotationGene

Type: object

Properties

gene: Type: object LinkedReference
geneComponents: Type: array geneComponents

List of Gene Components
geneWid: Type: string

Gene Row ID
hgvs: Type: array hgvs

List og HGVS Notations
hugoName: Type: string

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

Nested Schema : LinkedReference

Type: object

Properties

display: Type: string
reference: Type: string

Nested Schema : geneComponents

Type: array

List of Gene Components

Items

Type: object GeneComponent

Nested Schema : hgvs

Type: array

List og HGVS Notations

Items

Type: object Hgvs

Nested Schema : GeneComponent

Type: object

Properties

ensemblVersion: Type: string

Ensembl Version
transcripts: Type: array transcripts

List of Transcripts

Nested Schema : transcripts

Type: array

List of Transcripts

Items

Type: object Transcript

Nested Schema : Transcript

Type: object

Properties

componentTypes: Type: array componentTypes

List of Component Types
transcriptId: Type: string

Transcript ID

Nested Schema : componentTypes

Type: array

List of Component Types

Items

Type: string

Nested Schema : Hgvs

Type: object

Properties

ensemblVersion: Type: string

Ensembl Version
hgvsNotations: Type: array hgvsNotations

List of HGVS Notations

Nested Schema : hgvsNotations

Type: array

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:7001/HSDataService-web/api/3.2.0/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" : "/HSDataService-web/api/3.2.0/genes/137"
    }
  }, {
    "geneWid" : "138",
    "hugoName" : "RP1-283E3.8",
    "geneComponents" : [ {
      "ensemblVersion" : "GRCH37.75",
      "transcripts" : [ {
        "componentTypes" : [ "exon" ]
      }, {
        "transcriptId" : "ENST00000598846",
        "componentTypes" : [ "misc_RNA" ]
      } ]
    } ],
    "gene" : {
      "reference" : "/HSDataService-web/api/3.2.0/genes/138"
    }
  } ],
  "variantXref" : {
    "reference" : "/HSDataService-web/api/3.2.0/variants/31486/variantXRef"
  },
  "variantPrediction" : {
    "reference" : "/HSDataService-web/api/3.2.0/variants/31486/variantPredictions"
  },
  "variantEffect" : {
    "reference" : "/HSDataService-web/api/3.2.0/variants/31486/variantEffects"
  },
  "diseaseVariants" : {
    "reference" : "/HSDataService-web/api/3.2.0/variants/31486/diseases"
  },
  "cancerVariants" : {
    "reference" : "/HSDataService-web/api/3.2.0/variants/31486/cancer"
  }
}