Genomics Reporting Implementation Guide
3.0.0 - STU3 International flag

This page is part of the Genetic Reporting Implementation Guide (v3.0.0: STU3) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version. For a full list of available versions, see the Directory of published versions

: FindSubjectMolecConseqOutput - XML Representation

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<Parameters xmlns="http://hl7.org/fhir">
  <id value="FindSubjectMolecConseqOutput"/>
  <parameter>
    <name value="consequence"/>
    <resource>
      <Observation>
        <id value="MC1"/>
        <meta>
          <profile
                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"/>
        </meta>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml">NM_001395525.1:c.-281+2T>C - intronic_variant:loss_of_function_variant</div>
        </text>
        <status value="final"/>
        <category>
          <coding>
            <system
                    value="http://terminology.hl7.org/CodeSystem/observation-category"/>
            <code value="laboratory"/>
          </coding>
        </category>
        <category>
          <coding>
            <system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
            <code value="GE"/>
          </coding>
        </category>
        <code>
          <coding>
            <system
                    value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
            <code value="molecular-consequence"/>
          </coding>
        </code>
        <subject>🔗 
          <reference value="Patient/HG00403"/>
        </subject>
        <effectiveDateTime value="2023-04-01"/>
        <performer>🔗 
          <reference value="Organization/ExampleOrg"/>
        </performer>
        <interpretation>
          <coding>
            <system
                    value="http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#impact-prediction"/>
            <code value="HIGH"/>
            <display value="High"/>
          </coding>
        </interpretation>
        <derivedFrom>
          <reference value="Observation/variantExampleMC"/>
        </derivedFrom>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="51958-7"/>
              <display value="Transcript reference sequence [ID]"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
              <code value="NM_001395525.1"/>
              <display value="NM_001395525.1"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system
                      value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
              <code value="feature-consequence"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.sequenceontology.org"/>
              <code value="SO:0001575"/>
              <display value="splice_donor_variant"/>
            </coding>
            <coding>
              <system value="http://www.sequenceontology.org"/>
              <code value="SO:0001627"/>
              <display value="intron_variant"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system
                      value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
              <code value="functional-effect"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.sequenceontology.org"/>
              <code value="SO_0002054"/>
              <display value="loss_of_function_variant"/>
            </coding>
          </valueCodeableConcept>
        </component>
      </Observation>
    </resource>
  </parameter>
  <parameter>
    <name value="consequence"/>
    <resource>
      <Observation>
        <id value="MC2"/>
        <meta>
          <profile
                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"/>
        </meta>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml">NM_001366781.1:c.90T>C - synonymous_variant</div>
        </text>
        <status value="final"/>
        <category>
          <coding>
            <system
                    value="http://terminology.hl7.org/CodeSystem/observation-category"/>
            <code value="laboratory"/>
          </coding>
        </category>
        <category>
          <coding>
            <system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
            <code value="GE"/>
          </coding>
        </category>
        <code>
          <coding>
            <system
                    value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
            <code value="molecular-consequence"/>
          </coding>
        </code>
        <subject>🔗 
          <reference value="Patient/HG00403"/>
        </subject>
        <effectiveDateTime value="2023-04-01"/>
        <performer>🔗 
          <reference value="Organization/ExampleOrg"/>
        </performer>
        <interpretation>
          <coding>
            <system
                    value="http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#impact-prediction"/>
            <code value="LOW"/>
            <display value="Low"/>
          </coding>
        </interpretation>
        <derivedFrom>
          <reference value="Observation/variantExampleMC"/>
        </derivedFrom>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48004-6"/>
            </coding>
            <text value="coding HGVS"/>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://varnomen.hgvs.org"/>
              <code value="NM_001366781.1:c.90T&gt;C"/>
              <display value="NM_001366781.1:c.90T&gt;C"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="51958-7"/>
              <display value="Transcript reference sequence [ID]"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
              <code value="NM_001366781.1"/>
              <display value="NM_001366781.1"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system
                      value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
              <code value="feature-consequence"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.sequenceontology.org"/>
              <code value="SO:0001819"/>
              <display value="synonymous_variant"/>
            </coding>
          </valueCodeableConcept>
        </component>
      </Observation>
    </resource>
  </parameter>
  <parameter>
    <name value="consequence"/>
    <resource>
      <Observation>
        <id value="MC3"/>
        <meta>
          <profile
                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"/>
        </meta>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml">Molecular Consequence</div>
        </text>
        <status value="final"/>
        <category>
          <coding>
            <system
                    value="http://terminology.hl7.org/CodeSystem/observation-category"/>
            <code value="laboratory"/>
          </coding>
        </category>
        <category>
          <coding>
            <system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
            <code value="GE"/>
          </coding>
        </category>
        <code>
          <coding>
            <system
                    value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
            <code value="molecular-consequence"/>
          </coding>
        </code>
        <subject>🔗 
          <reference value="Patient/HG00403"/>
        </subject>
        <effectiveDateTime value="2023-04-01"/>
        <performer>🔗 
          <reference value="Organization/ExampleOrg"/>
        </performer>
        <interpretation>
          <coding>
            <system
                    value="http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#impact-prediction"/>
            <code value="MOD"/>
            <display value="Modifier"/>
          </coding>
        </interpretation>
        <derivedFrom>
          <reference value="Observation/variantExampleMC"/>
        </derivedFrom>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48004-6"/>
            </coding>
            <text value="coding HGVS"/>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://varnomen.hgvs.org"/>
              <code value="NM_001395543.1:c.-171T&gt;C"/>
              <display value="NM_001395543.1:c.-171T&gt;C"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="51958-7"/>
              <display value="Transcript reference sequence [ID]"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
              <code value="NM_001395543.1"/>
              <display value="NM_001395543.1"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system
                      value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
              <code value="feature-consequence"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.sequenceontology.org"/>
              <code value="SO:0001623"/>
              <display value="5_prime_UTR_variant"/>
            </coding>
          </valueCodeableConcept>
        </component>
      </Observation>
    </resource>
  </parameter>
  <parameter>
    <name value="consequence"/>
    <resource>
      <Observation>
        <id value="MC4"/>
        <meta>
          <profile
                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"/>
        </meta>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml">Molecular Consequence</div>
        </text>
        <status value="final"/>
        <category>
          <coding>
            <system
                    value="http://terminology.hl7.org/CodeSystem/observation-category"/>
            <code value="laboratory"/>
          </coding>
        </category>
        <category>
          <coding>
            <system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
            <code value="GE"/>
          </coding>
        </category>
        <code>
          <coding>
            <system
                    value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
            <code value="molecular-consequence"/>
          </coding>
        </code>
        <subject>🔗 
          <reference value="Patient/HG00403"/>
        </subject>
        <effectiveDateTime value="2023-04-01"/>
        <performer>🔗 
          <reference value="Organization/ExampleOrg"/>
        </performer>
        <interpretation>
          <coding>
            <system
                    value="http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#impact-prediction"/>
            <code value="MOD"/>
            <display value="Modifier"/>
          </coding>
        </interpretation>
        <derivedFrom>
          <reference value="Observation/variantExampleMC"/>
        </derivedFrom>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="51958-7"/>
              <display value="Transcript reference sequence [ID]"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
              <code value="NM_001395544.1"/>
              <display value="NM_001395544.1"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system
                      value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
              <code value="feature-consequence"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.sequenceontology.org"/>
              <code value="SO:0001627"/>
              <display value="intron_variant"/>
            </coding>
          </valueCodeableConcept>
        </component>
      </Observation>
    </resource>
  </parameter>
  <parameter>
    <name value="variant"/>
    <resource>
      <Observation>
        <id value="variantExampleMC"/>
        <meta>
          <profile
                   value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
        </meta>
        <text>
          <status value="generated"/>
          <div xmlns="http://www.w3.org/1999/xhtml">Variant</div>
        </text>
        <status value="final"/>
        <category>
          <coding>
            <system
                    value="http://terminology.hl7.org/CodeSystem/observation-category"/>
            <code value="laboratory"/>
          </coding>
        </category>
        <category>
          <coding>
            <system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
            <code value="GE"/>
          </coding>
        </category>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="69548-6"/>
            <display value="Genetic variant assessment"/>
          </coding>
        </code>
        <subject>🔗 
          <reference value="Patient/HG00403"/>
        </subject>
        <effectiveDateTime value="2023-04-01"/>
        <performer>🔗 
          <reference value="Organization/ExampleOrg"/>
        </performer>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA9633-4"/>
            <display value="Present"/>
          </coding>
        </valueCodeableConcept>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48002-0"/>
              <display value="Genomic source class"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://loinc.org"/>
              <code value="LA6683-2"/>
              <display value="Germline"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="48013-7"/>
              <display value="Genomic reference sequence ID"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
              <code value="NC_000001.10"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="53034-5"/>
              <display value="Allelic state"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://loinc.org"/>
              <code value="LA6706-1"/>
              <display value="Heterozygous"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="81252-9"/>
              <display value="Discrete genetic variant"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://varnomen.hgvs.org"/>
              <code value="NC_000001.10:g.86852621A&gt;G"/>
              <display value="NC_000001.10:g.86852621A&gt;G"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="81258-6"/>
              <display value="Sample VAF"/>
            </coding>
          </code>
          <valueQuantity>
            <value value="0.6"/>
            <unit
                  value="relative frequency of a particular allele in the specimen"/>
            <system value="http://unitsofmeasure.org"/>
            <code value="1"/>
          </valueQuantity>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="69547-8"/>
              <display value="Genomic Ref allele [ID]"/>
            </coding>
          </code>
          <valueString value="A"/>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="69551-0"/>
              <display value="Genomic Alt allele [ID]"/>
            </coding>
          </code>
          <valueString value="G"/>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="92822-6"/>
              <display value="Genomic coord system"/>
            </coding>
          </code>
          <valueCodeableConcept>
            <coding>
              <system value="http://loinc.org"/>
              <code value="LA30100-4"/>
              <display value="0-based interval counting"/>
            </coding>
          </valueCodeableConcept>
        </component>
        <component>
          <code>
            <coding>
              <system value="http://loinc.org"/>
              <code value="81254-5"/>
              <display value="Genomic allele start-end"/>
            </coding>
          </code>
          <valueRange>
            <low>
              <value value="86852620"/>
            </low>
          </valueRange>
        </component>
      </Observation>
    </resource>
  </parameter>
</Parameters>