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FHIR IG analytics

Packagefhir.deep6.ai
Resource TypeObservation
IdObservation-example-variant-hgvs.json
FHIR VersionR4

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Narrative

Note: links and images are rebased to the (stated) source

Generated Narrative: Observation example-variant-hgvs

status: Final

category: Laboratory, Genetics

code: Genetic variant assessment

subject: abc Hilll811 (maiden) Female, DoB: 1988-05-10 ( https://github.com/synthetichealth/synthea#761b29e0-dac6-9b2b-2970-62289a517a3e)

effective: 2023-05-09 20:26:11+0000

method: Sequencing

component

code: DNA change type

value: SNV

component

code: Gene studied [ID]

value: TP53

component

code: Amino acid change (pHGVS)

value: NM_000546.5:p.P278S

component

code: DNA change (c.HGVS)

value: NM_000546.5:c.832C>T


Source1

{
  "resourceType": "Observation",
  "id": "example-variant-hgvs",
  "meta": {
    "profile": [
      "http://deep6.ai/fhir/StructureDefinition/deep-6-ai-variant-2.1.0"
    ]
  },
  "text": {
    "status": "generated",
    "div": "<!-- snip (see above) -->"
  },
  "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",
          "display": "Genetics"
        }
      ]
    }
  ],
  "code": {
    "coding": [
      {
        "system": "http://loinc.org",
        "code": "69548-6",
        "display": "Genetic variant assessment"
      }
    ]
  },
  "subject": {
    "reference": "Patient/patient-example"
  },
  "effectiveDateTime": "2023-05-09T20:26:11Z",
  "method": {
    "coding": [
      {
        "system": "http://loinc.org",
        "code": "LA26398-0",
        "display": "Sequencing"
      }
    ]
  },
  "component": [
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "48019-4",
            "display": "DNA change type"
          }
        ]
      },
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://www.sequenceontology.org",
            "code": "SO:0001483",
            "display": "SNV"
          }
        ]
      }
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "48018-6",
            "display": "Gene studied [ID]"
          }
        ]
      },
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://www.genenames.org",
            "code": "HGNC:11998"
          }
        ],
        "text": "TP53"
      }
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "48005-3",
            "display": "Amino acid change (pHGVS)"
          }
        ]
      },
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://varnomen.hgvs.org",
            "code": "NM_000546.5:p.P278S"
          }
        ]
      }
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "48004-6",
            "display": "DNA change (c.HGVS)"
          }
        ]
      },
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://varnomen.hgvs.org",
            "code": "NM_000546.5:c.832C>T"
          }
        ]
      }
    }
  ]
}