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Retrieve Variant Effects for a Variant Identifier

get

/ohfapi/cg/v3.3/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: integer(int64)
  Variant Row ID

Security

• basicAuth: basic
  Type: basic

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Response

Supported Media Types

• application/json
• application/xml

200 Response

successful operation

Body ()

Root Schema : VariantEffects

Type: object

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• gene(optional): array gene
  List of Genes
• identifier(optional): object Identifier
  Identifier assigned by a given system
• resourceType(optional): string
• variantReferences(optional): object LinkedReference

{
    "type":"object",
    "properties":{
        "resourceType":{
            "type":"string"
        },
        "identifier":{
            "description":"Variant Row ID",
            "$ref":"#/definitions/Identifier"
        },
        "gene":{
            "type":"array",
            "description":"List of Genes",
            "items":{
                "$ref":"#/definitions/VariantGene"
            }
        },
        "variantReferences":{
            "example":"{href: '/variants/{variantRecordId}'}",
            "description":"A link containing href to retrieve Variant Annotation details",
            "$ref":"#/definitions/LinkedReference"
        }
    }
}

Nested Schema : gene

Type: array

List of Genes

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• Array of: object VariantGene

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

Nested Schema : Identifier

Type: object

Identifier assigned by a given system

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• 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 : LinkedReference

Type: object

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

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

Nested Schema : VariantGene

Type: object

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• hugoName(optional): string
  Approved HUGO symbol for species loci, including protein coding genes, RNA genes and pseudogenes, e.g. 'SRY', 'DMRT1', 'FOXL2', etc.
• variantEffect(optional): array variantEffect
  List of Variant Effects

{
    "type":"object",
    "properties":{
        "hugoName":{
            "type":"string",
            "description":"Approved HUGO symbol for species loci, including protein coding genes, RNA genes and pseudogenes, e.g. 'SRY', 'DMRT1', 'FOXL2', etc. "
        },
        "variantEffect":{
            "type":"array",
            "description":"List of Variant Effects",
            "items":{
                "$ref":"#/definitions/VariantEffect"
            }
        }
    }
}

Nested Schema : variantEffect

Type: array

List of Variant Effects

Show Source

• Array of: object VariantEffect

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

Nested Schema : VariantEffect

Type: object

Show Source

• aminoAcidChange(optional): string
  Protein Effect. For ex.,p.(195PAdelinsRT)
• assembly(optional): string
  Assembly/Alignment Name. For ex.,GRCh38
• ensemblVersion(optional): string
  Ensembl Version. For ex.,GRCH37.75
• netEffect(optional): string
  Net Effect. For ex.,non-coding
• transcriptId(optional): string
  Transcript ID. For.,ENST00000441069

{
    "type":"object",
    "properties":{
        "transcriptId":{
            "type":"string",
            "description":"Transcript ID. For.,ENST00000441069"
        },
        "assembly":{
            "type":"string",
            "description":"Assembly/Alignment Name. For ex.,GRCh38"
        },
        "ensemblVersion":{
            "type":"string",
            "description":"Ensembl Version. For ex.,GRCH37.75"
        },
        "netEffect":{
            "type":"string",
            "description":"Net Effect. For ex.,non-coding"
        },
        "aminoAcidChange":{
            "type":"string",
            "description":"Protein Effect. For ex.,p.(195PAdelinsRT)"
        }
    }
}

400 Response

Variant Id is not supplied

404 Response

Variant effect(s) not found

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Examples

The following example submits a GET request.

API URL

http://localhost:7010/ohfapi/cg/v3.3/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" : "/ohfapi/cg/v3.3/variants/7838"
  }
}

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