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FHIR IG analytics

Packagefhir.nwgenomics.nhs.uk
Resource TypeObservation
IdObservation-ctdna9737383222-icnv1.json
FHIR VersionR4

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Narrative

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

Generated Narrative: Observation ctdna9737383222-icnv1

identifier: ctdna9737383222-icnv1

status: Final

category: Genetics, Laboratory

code: Genetic variant assessment

subject: Rob LEEDS (official) Male, DoB: 1978-01-17 ( Medical record number: L765432)

effective: 2026-07-14 15:59:16+0000

performer: Result INTERPRETER at North West Genomics

value: Present

method: Sequencing

component

code: Variant category

value: Intragenic Copy Number Variant

component

code: Gene studied [ID]

value: FBN1

component

code: Genomic source class [Type]

value: Germline

component

code: Genomic reference sequence [ID]

value: NC_000015.9

component

code: Genomic coordinate system [Type]

value: 1-based character counting

component

code: Genomic ref allele [ID]

value: C

component

code: Genomic alt allele [ID]

value: <DEL>

component

code: DNA change type

value: copy_number_variation

component

code: Transcript reference sequence [ID]

value: NM_000138.4

component

code: DNA change (c.HGVS)

value: NM_000138.4(FBN1):exon13_to_exon15del

component

code: Genomic DNA change (gHGVS)

value: g.48797222_48802366del

component

code: Genetic variation clinical significance [Imp]

value: Pathogenic

component

code: Origin of germline genetic variant [Type]

value: Maternal

component

code: Structural variant inner start and end

value: 48797221-48802366

component

code: Sample variant allelic frequency [NFr]

value: 0.33 decimal

component

code: Genomic structural variant copy number

value: 1 1 (Details: UCUM code1 = '1')


Source1

{
  "resourceType": "Observation",
  "id": "ctdna9737383222-icnv1",
  "meta": {
    "profile": [
      "https://fhir.nwgenomics.nhs.uk/StructureDefinition/Variant"
    ]
  },
  "text": {
    "status": "generated",
    "div": "<!-- snip (see above) -->"
  },
  "identifier": [
    {
      "value": "ctdna9737383222-icnv1"
    }
  ],
  "status": "final",
  "category": [
    {
      "coding": [
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          "system": "http://terminology.hl7.org/CodeSystem/v2-0074",
          "code": "GE",
          "display": "Genetics"
        }
      ]
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          "code": "laboratory"
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  "code": {
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        "code": "69548-6"
      }
    ]
  },
  "subject": {
    "reference": "Patient/Patient-Leeds"
  },
  "effectiveDateTime": "2026-07-14T15:59:16+00:00",
  "performer": [
    {
      "reference": "PractitionerRole/59577028-8fcc-4554-8b43-988561d41d9c"
    }
  ],
  "valueCodeableConcept": {
    "coding": [
      {
        "system": "http://loinc.org",
        "code": "LA9633-4",
        "display": "Present"
      }
    ]
  },
  "method": {
    "coding": [
      {
        "system": "http://loinc.org",
        "code": "LA26398-0",
        "display": "Sequencing"
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    ]
  },
  "component": [
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "83005-9",
            "display": "Variant category"
          }
        ]
      },
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "https://fhir.nwgenomics.nhs.uk/CodeSystem/IGeneVariantCategory",
            "code": "ICNV",
            "display": "Intragenic Copy Number Variant"
          }
        ]
      }
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "48018-6",
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      "valueCodeableConcept": {
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            "code": "HGNC:3603",
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        ]
      }
    },
    {
      "code": {
        "coding": [
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      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "LA6683-2",
            "display": "Germline"
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        ]
      }
    },
    {
      "code": {
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          {
            "system": "http://loinc.org",
            "code": "48013-7",
            "display": "Genomic reference sequence [ID]"
          }
        ]
      },
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://www.ncbi.nlm.nih.gov/refseq",
            "code": "NC_000015.9"
          }
        ]
      }
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "92822-6",
            "display": "Genomic coordinate system [Type]"
          }
        ]
      },
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "LA30102-0",
            "display": "1-based character counting"
          }
        ]
      }
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "69547-8",
            "display": "Genomic ref allele [ID]"
          }
        ]
      },
      "valueString": "C"
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "69551-0",
            "display": "Genomic alt allele [ID]"
          }
        ]
      },
      "valueString": "<DEL>"
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "48019-4",
            "display": "DNA change type"
          }
        ]
      },
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://www.sequenceontology.org",
            "code": "SO:0001019",
            "display": "copy_number_variation"
          }
        ]
      }
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "51958-7",
            "display": "Transcript reference sequence [ID]"
          }
        ]
      },
      "valueCodeableConcept": {
        "coding": [
          {
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            "code": "NM_000138.4"
          }
        ]
      }
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "48004-6",
            "display": "DNA change (c.HGVS)"
          }
        ]
      },
      "valueCodeableConcept": {
        "coding": [
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            "code": "NM_000138.4(FBN1):exon13_to_exon15del"
          }
        ]
      }
    },
    {
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            "system": "http://loinc.org",
            "code": "81290-9",
            "display": "Genomic DNA change (gHGVS)"
          }
        ]
      },
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://varnomen.hgvs.org",
            "code": "g.48797222_48802366del"
          }
        ]
      }
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "53037-8",
            "display": "Genetic variation clinical significance [Imp]"
          }
        ]
      },
      "valueCodeableConcept": {
        "text": "Pathogenic"
      }
    },
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "94186-4",
            "display": "Origin of germline genetic variant [Type]"
          }
        ]
      },
      "valueCodeableConcept": {
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    },
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            "system": "http://loinc.org",
            "code": "81302-2",
            "display": "Structural variant inner start and end"
          }
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        },
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        }
      }
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        "unit": "decimal",
        "system": "http://unitsofmeasure.org"
      }
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          }
        ]
      },
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        "system": "http://unitsofmeasure.org",
        "code": "1"
      }
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  ]
}