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

(back to narrative)

Raw json

{
  "resourceType" : "CodeSystem",
  "id" : "genetic-coordinate-system",
  "text" : {
    "status" : "generated",
    "div" : "<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>"
  },
  "url" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genetic-coordinate-system",
  "version" : "0.3.0",
  "name" : "GeneticCoordinateSystem",
  "status" : "draft",
  "experimental" : false,
  "date" : "2018-12-04T11:36:15+11:00",
  "contact" : [
    {
      "telecom" : [
        {
          "system" : "url"
        },
        {
          "system" : "email"
        }
      ]
    }
  ],
  "description" : "Base coordinate systems start and end measurements for variants",
  "jurisdiction" : [
    {
      "coding" : [
        {
          "system" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
          "code" : "001",
          "display" : "World"
        }
      ]
    }
  ],
  "caseSensitive" : true,
  "valueSet" : "http://hl7.org/fhir/uv/genomics-reporting/ValueSet/genetic-coordinate-system",
  "content" : "complete",
  "concept" : [
    {
      "code" : "Interval",
      "display" : "Interval",
      "definition" : "0-based numbering or interbase coordinate system, inclusive start, exclusive end"
    },
    {
      "code" : "Variant method",
      "display" : "Variant method",
      "definition" : "1-based [inclusive start, inclusive end] - with Alignment Method (VCF-like)"
    },
    {
      "code" : "Alignment method",
      "display" : "Alignment method",
      "definition" : "1-based [inclusive start, inclusive end] - with Variant Method (HGVS-like)"
    }
  ]
}