REST API for Oracle Healthcare Translational Research

Retrieve Variant Effects for a Variant Identifier

get

/HSDataService-web/api/3.2.0/variants/{id}/variantEffects

This endpoint supports the retrieval of Variant Effects by Variant Identifier. The returns Variant Effect information like HUGO Name, Transcript Identifier, Assembly/Alignment Name, Ensembl Version, Amino Acid Change and other Variant Effect associated information.

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 : VariantEffects

Type: object

Properties

gene: Type: array gene

List of Genes
identifier: Type: object Identifier

Identifier assigned by a given system
resourceType: Type: string
variantReferences: Type: object LinkedReference

Nested Schema : gene

Type: array

List of Genes

Items

Type: object VariantGene

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 : LinkedReference

Type: object

Properties

display: Type: string
reference: Type: string

Nested Schema : VariantGene

Type: object

Properties

hugoName: Type: string

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

List of Variant Effects

Nested Schema : variantEffect

Type: array

List of Variant Effects

Items

Type: object VariantEffect

Nested Schema : VariantEffect

Type: object

Properties

aminoAcidChange: Type: string

Protein Effect. For ex.,p.(195PAdelinsRT)
assembly: Type: string

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

Ensembl Version. For ex.,GRCH37.75
netEffect: Type: string

Net Effect. For ex.,non-coding
transcriptId: Type: string

Transcript ID. For.,ENST00000441069

400 Response

Variant Id is not supplied

404 Response

Variant effect(s) not found

Examples

The following example submits a GET request.

API URL

http://localhost:7001/HSDataService-web/api/3.2.0/variants/7838/variantEffects

Example of Response Body

The following example shows the response returned in JSON format.

{
"resourceType" : "VariantEffects",
  "identifier" : {
    "system" : "ODB",
    "value" : "7838"
  },
  "gene" : [ {
    "hugoName" : "SAMD11",
    "variantEffect" : [ {
      "transcriptId" : "ENST00000341065",
      "assembly" : "GRCh37",
      "ensemblVersion" : "GRCH37.75",
      "netEffect" : "synonymous",
      "aminoAcidChange" : "p.(518=)"
    }, {
      "transcriptId" : "ENST00000342066",
      "assembly" : "GRCh37",
      "ensemblVersion" : "GRCH37.75",
      "netEffect" : "synonymous",
      "aminoAcidChange" : "p.(610=)"
    }, {
      "transcriptId" : "ENST00000455979",
      "assembly" : "GRCh37",
      "ensemblVersion" : "GRCH37.75",
      "netEffect" : "synonymous",
      "aminoAcidChange" : "p.(470=)"
    } ]
  } ],
  "variantReferences" : {
    "reference" : "/HSDataService-web/api/3.2.0/variants/7838"
  }
}