Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

## : ATR-insertion-var - TTL Representation

Page standards status: Informative

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    @prefix fhir: <http://hl7.org/fhir/> .
    @prefix loinc: <https://loinc.org/rdf/> .
    @prefix owl: <http://www.w3.org/2002/07/owl#> .
    @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
    @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
    @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

    # - resource -------------------------------------------------------------------

     a fhir:Observation ;
      fhir:nodeRole fhir:treeRoot ;
      fhir:id [ fhir:v "ATR-insertion-var"] ; #
      fhir:meta [
        ( fhir:profile [
    fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"^^xsd:anyURI ;
    fhir:l <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant>     ] )
      ] ; #
      fhir:text [
    fhir:status [ fhir:v "generated" ] ;
    fhir:div [ fhir:v "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Observation ATR-insertion-var</b></p><a name=\"ATR-insertion-var\"> </a><a name=\"hcATR-insertion-var\"> </a><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\"/><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-variant.html\">Variant</a></p></div><p><b>status</b>: Final</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></p><p><b>subject</b>: <a href=\"Patient-somaticPatient.html\">Substance Junior Hamsburg (official) Male, DoB: 1987-09-01 ( Medical record number: 1234567 (use: temp, period: 2021-01-01 --&gt; (ongoing)))</a></p><p><b>effective</b>: 2023-02-01</p><p><b>performer</b>: <a href=\"Practitioner-pathologistPractitioner.html\">Practitioner Test Dolin </a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><p><b>method</b>: <span title=\"Codes:{http://loinc.org LA26398-0}\">Sequencing</span></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51958-7}\">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_001184.4}\">NM_001184.4</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 82121-5}\">Allelic read depth</span></p><p><b>value</b>: 131 reads per base pair<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM  code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48019-4}\">DNA change type</span></p><p><b>value</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:0000667}\">insertion</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48004-6}\">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NM_001184.4:c.2878_2879insAGTAA}\">NM_001184.4:c.2878_2879insAGTAA</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48018-6}\">Gene studied [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.genenames.org HGNC:882}\">ATR</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69551-0}\">Genomic alt allele [ID]</span></p><p><b>value</b>: TTACT</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48000-4}\">Chromosome [Identifier] in Blood or Tissue by Molecular genetics method</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA21256-5}\">Chromosome 3</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81254-5}\">Genomic allele start-end</span></p><p><b>value</b>: 142269071-142269071</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48013-7}\">Genomic reference sequence [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NC_000003.11}\">NC_000003.11</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81290-9}\">Genomic DNA change (gHGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NC_000003.11:g.142269071_142269072insTTACT}\">NC_000003.11:g.142269071_142269072insTTACT</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48002-0}\">Genomic source class [Type]</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6684-0}\">Somatic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81258-6}\">Sample variant allelic frequency [NFr]</span></p><p><b>value</b>: 0.075 decimal</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs conclusion-string}\">Conclusion Text</span></p><p><b>value</b>: Gene: ATR; Exon: 14; Nucleotide: NM_001184.4:c.2878_2879insAGTAA; Genomic Location: NC_000003.11:g.142269071_142269072insTTACT; Amino acid: NP_001175.2:p.R960fs*2; Function: loss; Assessment: Likely Pathogenic; Classification: Tier 2C; Allele Fraction: 5.34% (of 131 reads); Variation: Insertion; Interpretation: The protein encoded by this gene is a serine/threonine kinase and DNA damage sensor, activating cell cycle checkpoint signaling upon DNA stress. The encoded protein can phosphorylate and activate several proteins involved ... more</p></blockquote></div>"^^rdf:XMLLiteral ]
      ] ; #
      fhir:status [ fhir:v "final"] ; #
      fhir:category ( [
        ( fhir:coding [
    fhir:system [
    fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ;
    fhir:l <http://terminology.hl7.org/CodeSystem/observation-category>       ] ;
    fhir:code [ fhir:v "laboratory" ]     ] )
      ] [
        ( fhir:coding [
    fhir:system [
    fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ;
    fhir:l <http://terminology.hl7.org/CodeSystem/v2-0074>       ] ;
    fhir:code [ fhir:v "GE" ]     ] )
      ] ) ; #
      fhir:code [
        ( fhir:coding [
    a loinc:69548-6 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>       ] ;
    fhir:code [ fhir:v "69548-6" ]     ] )
      ] ; #
      fhir:subject [
    fhir:l fhir:Patient/somaticPatient ;
    fhir:reference [ fhir:v "Patient/somaticPatient" ]
      ] ; #
      fhir:effective [
    a fhir:DateTime ;
    fhir:v "2023-02-01"^^xsd:date
      ] ; #
      fhir:performer ( [
    fhir:l fhir:Practitioner/pathologistPractitioner ;
    fhir:reference [ fhir:v "Practitioner/pathologistPractitioner" ]
      ] ) ; #
      fhir:value [
    a fhir:CodeableConcept ;
        ( fhir:coding [
    a loinc:LA9633-4 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>       ] ;
    fhir:code [ fhir:v "LA9633-4" ] ;
    fhir:display [ fhir:v "Present" ]     ] )
      ] ; #
      fhir:method [
        ( fhir:coding [
    a loinc:LA26398-0 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>       ] ;
    fhir:code [ fhir:v "LA26398-0" ] ;
    fhir:display [ fhir:v "Sequencing" ]     ] )
      ] ; #
      fhir:component ( [
    fhir:code [
          ( fhir:coding [
    a loinc:51958-7 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "51958-7" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    fhir:system [
    fhir:v "http://www.ncbi.nlm.nih.gov/refseq"^^xsd:anyURI ;
    fhir:l <http://www.ncbi.nlm.nih.gov/refseq>         ] ;
    fhir:code [ fhir:v "NM_001184.4" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:82121-5 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "82121-5" ]       ] )     ] ;
    fhir:value [
    a fhir:Quantity ;
    fhir:value [ fhir:v "131"^^xsd:decimal ] ;
    fhir:unit [ fhir:v "reads per base pair" ] ;
    fhir:system [
    fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ;
    fhir:l <http://unitsofmeasure.org>       ] ;
    fhir:code [ fhir:v "1" ]     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:48019-4 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "48019-4" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    fhir:system [
    fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ;
    fhir:l <http://www.sequenceontology.org>         ] ;
    fhir:code [ fhir:v "SO:0000667" ] ;
    fhir:display [ fhir:v "insertion" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:48004-6 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "48004-6" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    fhir:system [
    fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ;
    fhir:l <http://varnomen.hgvs.org>         ] ;
    fhir:code [ fhir:v "NM_001184.4:c.2878_2879insAGTAA" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:48018-6 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "48018-6" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    fhir:system [
    fhir:v "http://www.genenames.org"^^xsd:anyURI ;
    fhir:l <http://www.genenames.org>         ] ;
    fhir:code [ fhir:v "HGNC:882" ] ;
    fhir:display [ fhir:v "ATR" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:69551-0 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "69551-0" ]       ] )     ] ;
    fhir:value [
    a fhir:String ;
    fhir:v "TTACT"     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:48000-4 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "48000-4" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    a loinc:LA21256-5 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "LA21256-5" ] ;
    fhir:display [ fhir:v "Chromosome 3" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:81254-5 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "81254-5" ]       ] )     ] ;
    fhir:value [
    a fhir:Range ;
    fhir:low [
    fhir:value [ fhir:v "142269071"^^xsd:decimal ]       ] ;
    fhir:high [
    fhir:value [ fhir:v "142269071"^^xsd:decimal ]       ]     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:48013-7 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "48013-7" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    fhir:system [
    fhir:v "http://www.ncbi.nlm.nih.gov/refseq"^^xsd:anyURI ;
    fhir:l <http://www.ncbi.nlm.nih.gov/refseq>         ] ;
    fhir:code [ fhir:v "NC_000003.11" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:81290-9 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "81290-9" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    fhir:system [
    fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ;
    fhir:l <http://varnomen.hgvs.org>         ] ;
    fhir:code [ fhir:v "NC_000003.11:g.142269071_142269072insTTACT" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:48002-0 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "48002-0" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    a loinc:LA6684-0 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "LA6684-0" ] ;
    fhir:display [ fhir:v "Somatic" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:81258-6 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "81258-6" ]       ] )     ] ;
    fhir:value [
    a fhir:Quantity ;
    fhir:value [ fhir:v 0.075 ] ;
    fhir:unit [ fhir:v "decimal" ] ;
    fhir:system [
    fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ;
    fhir:l <http://unitsofmeasure.org>       ]     ]
      ] [
    fhir:code [
          ( fhir:coding [
    fhir:system [
    fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ;
    fhir:l <http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs>         ] ;
    fhir:code [ fhir:v "conclusion-string" ]       ] )     ] ;
    fhir:value [
    a fhir:String ;
    fhir:v "Gene: ATR; Exon: 14; Nucleotide: NM_001184.4:c.2878_2879insAGTAA; Genomic Location: NC_000003.11:g.142269071_142269072insTTACT; Amino acid: NP_001175.2:p.R960fs*2; Function: loss; Assessment: Likely Pathogenic; Classification: Tier 2C; Allele Fraction: 5.34% (of 131 reads); Variation: Insertion; Interpretation: The protein encoded by this gene is a serine/threonine kinase and DNA damage sensor, activating cell cycle checkpoint signaling upon DNA stress. The encoded protein can phosphorylate and activate several proteins involved ... more"     ]
      ] ) . #