# Pgx-var-1020 - Genomics Reporting Implementation Guide v4.0.0-cibuild

* [**Table of Contents**](toc.md)
* [**Artifact List**](artifacts.md)
* **Pgx-var-1020**

## Example Observation: Pgx-var-1020

| |
| :--- |
| *Page standards status:*[Informative](http://hl7.org/fhir/R4/versions.html#std-process) |

Profile: [Variant](StructureDefinition-variant.md)

**status**: Final

**category**: Laboratory, Genetics

**code**: Genetic variant assessment

**subject**: [Adam B. Everyman Male, DoB: 1951-01-20 ( Medical Record Number: m123 (use: usual, ))](Patient-CGPatientExample01.md)

**effective**: 2019-04-01

**performer**: [Organization some lab](Organization-ExampleOrg.md)

**value**: Present

**note**: 

> 

This variant was confirmed with SANGER sequencing


**method**: Sequencing

> **component****code**:Genomic reference sequence [ID]**value**:b37 Chr10

> **component****code**:Genomic coordinate system [Type]**value**:1-based character counting

> **component****code**:Genomic allele start-end**value**: 96702047-96702047

> **component****code**:Genomic ref allele [ID]**value**: C

> **component****code**:Genomic alt allele [ID]**value**: C

> **component****code**:Genomic source class [Type]**value**:Germline

> **component****code**:Allelic state**value**:homozygous

> **component****code**:Gene studied [ID]**value**:CYP2C9

> **component****code**:DNA change type**value**:wild type

> **component****code**:Allelic read depth**value**: >20

> **component****code**:Variant Confidence Status**value**:High



## Resource Content

```json
{
  "resourceType" : "Observation",
  "id" : "Pgx-var-1020",
  "meta" : {
    "profile" : [
      "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
    ]
  },
  "status" : "final",
  "category" : [
    {
      "coding" : [
        {
          "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
          "code" : "laboratory"
        }
      ]
    },
    {
      "coding" : [
        {
          "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
          "code" : "GE"
        }
      ]
    }
  ],
  "code" : {
    "coding" : [
      {
        "system" : "http://loinc.org",
        "code" : "69548-6"
      }
    ]
  },
  "subject" : {
    "reference" : "Patient/CGPatientExample01"
  },
  "effectiveDateTime" : "2019-04-01",
  "performer" : [
    {
      "reference" : "Organization/ExampleOrg"
    }
  ],
  "valueCodeableConcept" : {
    "coding" : [
      {
        "system" : "http://loinc.org",
        "code" : "LA9633-4",
        "display" : "Present"
      }
    ]
  },
  "note" : [
    {
      "extension" : [
        {
          "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code",
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/coded-annotation-types-cs",
                "code" : "result-confirmation"
              }
            ]
          }
        }
      ],
      "text" : "This variant was confirmed with SANGER sequencing"
    }
  ],
  "method" : {
    "coding" : [
      {
        "system" : "http://loinc.org",
        "code" : "LA26398-0",
        "display" : "Sequencing"
      }
    ]
  },
  "component" : [
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "48013-7"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://www.ncbi.nlm.nih.gov/refseq",
            "code" : "NC_000010.10",
            "display" : "b37 Chr10"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "92822-6"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "LA30102-0",
            "display" : "1-based character counting"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "81254-5"
          }
        ]
      },
      "valueRange" : {
        "low" : {
          "value" : 96702047
        },
        "high" : {
          "value" : 96702047
        }
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "69547-8"
          }
        ]
      },
      "valueString" : "C"
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "69551-0"
          }
        ]
      },
      "valueString" : "C"
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "48002-0"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "LA6683-2",
            "display" : "Germline"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "53034-5"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "LA6705-3",
            "display" : "homozygous"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "48018-6"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://www.genenames.org",
            "code" : "HGNC:2623",
            "display" : "CYP2C9"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "48019-4"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://www.sequenceontology.org",
            "code" : "SO:1000002",
            "display" : "wild type"
          }
        ]
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "82121-5"
          }
        ]
      },
      "valueQuantity" : {
        "value" : 20,
        "comparator" : ">"
      }
    },
    {
      "code" : {
        "coding" : [
          {
            "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
            "code" : "variant-confidence-status"
          }
        ]
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://terminology.hl7.org/CodeSystem/variant-confidence-status-cs",
            "code" : "high"
          }
        ]
      }
    }
  ]
}

```
