This page is part of the Genetic Reporting Implementation Guide (v0.3.0: STU 1 Ballot 2) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

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Raw xml

<CodeSystem xmlns="http://hl7.org/fhir">
  <id value="genetic-coordinate-system"/>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><h2>GeneticCoordinateSystem</h2><div><p>Base coordinate systems start and end measurements for variants</p>
</div><p>This code system http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genetic-coordinate-system defines the following codes:</p><table class="codes"><tr><td style="white-space:nowrap"><b>Code</b></td><td><b>Display</b></td><td><b>Definition</b></td></tr><tr><td style="white-space:nowrap">Interval<a name="genetic-coordinate-system-Interval"> </a></td><td>Interval</td><td>0-based numbering or interbase coordinate system, inclusive start, exclusive end</td></tr><tr><td style="white-space:nowrap">Variant method<a name="genetic-coordinate-system-Variantmethod"> </a></td><td>Variant method</td><td>1-based [inclusive start, inclusive end] - with Alignment Method (VCF-like)</td></tr><tr><td style="white-space:nowrap">Alignment method<a name="genetic-coordinate-system-Alignmentmethod"> </a></td><td>Alignment method</td><td>1-based [inclusive start, inclusive end] - with Variant Method (HGVS-like)</td></tr></table></div>
  </text>
  <url
       value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genetic-coordinate-system"/>
  <version value="0.3.0"/>
  <name value="GeneticCoordinateSystem"/>
  <status value="draft"/>
  <experimental value="false"/>
  <date value="2018-12-04T11:36:15+11:00"/>
  <contact>
    <telecom>
      <system value="url"/>
    </telecom>
    <telecom>
      <system value="email"/>
    </telecom>
  </contact>
  <description
               value="Base coordinate systems start and end measurements for variants"/>
  <jurisdiction>
    <coding>
      <system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/>
      <code value="001"/>
      <display value="World"/>
    </coding>
  </jurisdiction>
  <caseSensitive value="true"/>
  <valueSet
            value="http://hl7.org/fhir/uv/genomics-reporting/ValueSet/genetic-coordinate-system"/>
  <content value="complete"/>
  <concept>
    <code value="Interval"/>
    <display value="Interval"/>
    <definition
                value="0-based numbering or interbase coordinate system, inclusive start, exclusive end"/>
  </concept>
  <concept>
    <code value="Variant method"/>
    <display value="Variant method"/>
    <definition
                value="1-based [inclusive start, inclusive end] - with Alignment Method (VCF-like)"/>
  </concept>
  <concept>
    <code value="Alignment method"/>
    <display value="Alignment method"/>
    <definition
                value="1-based [inclusive start, inclusive end] - with Variant Method (HGVS-like)"/>
  </concept>
</CodeSystem>