Clinical Genomics Resource Incubator
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Clinical Genomics Resource Incubator, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/cg-incubator/ and changes regularly. See the Directory of published versions

: Coordinate System Origin CodeSystem

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<CodeSystem xmlns="http://hl7.org/fhir">
  <id value="coordinatesystem-origin"/>
  <meta>
    <lastUpdated value="2026-03-13T00:00:00Z"/>
    <profile
             value="http://hl7.org/fhir/StructureDefinition/shareablecodesystem"/>
  </meta>
  <language value="en"/>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: CodeSystem coordinatesystem-origin</b></p><a name="coordinatesystem-origin"> </a><a name="hccoordinatesystem-origin"> </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">Last updated: 2026-03-13 00:00:00+0000</p><p style="margin-bottom: 0px">Profile: <a href="http://hl7.org/fhir/R5/shareablecodesystem.html">Shareable CodeSystem</a></p></div><p>This case-sensitive code system <code>http://hl7.org/fhir/uv/cg-incubator/CodeSystem/coordinatesystem-origin</code> 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">sequence-start<a name="coordinatesystem-origin-sequence-start"> </a></td><td>Sequence Start</td><td>Coordinates are measured from the start of the molecule: the 5' end of a nucleotide sequence or the N-terminus of a polypeptide. This is the default for genomic, chromosomal, and transcript-level coordinate systems (e.g., NC_ or NG_ accession-based positions).</td></tr><tr><td style="white-space:nowrap">cds-start<a name="coordinatesystem-origin-cds-start"> </a></td><td>CDS Start (A of ATG)</td><td>Coordinates are measured from the adenine of the translation initiation codon (A of ATG = position 1, or 0 in 0-based systems). This is the origin used by the HGVS coding DNA reference sequence (c. prefix). Positions upstream of the ATG are negative (5' UTR); positions downstream of the stop codon are marked with an asterisk (3' UTR).</td></tr><tr><td style="white-space:nowrap">feature-start<a name="coordinatesystem-origin-feature-start"> </a></td><td>Feature Start</td><td>Coordinates are measured from the start of a named genomic feature, such as the first base of an exon. This is used for HGVS exon-relative or feature-relative position expressions.</td></tr><tr><td style="white-space:nowrap">feature-end<a name="coordinatesystem-origin-feature-end"> </a></td><td>Feature End</td><td>Coordinates are measured from the end of a named genomic feature, such as the last base of an exon. A positive offset extends into the downstream intron; a negative offset extends upstream into the exon. This origin is used for HGVS intronic positions (e.g., c.100+3, where 100 is the last coding base and +3 is the offset into the intron).</td></tr></table></div>
  </text>
  <extension
             url="http://hl7.org/fhir/StructureDefinition/structuredefinition-wg">
    <valueCode value="cg"/>
  </extension>
  <extension
             url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
    <valueCode value="informative"/>
  </extension>
  <extension
             url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm">
    <valueInteger value="0"/>
  </extension>
  <url
       value="http://hl7.org/fhir/uv/cg-incubator/CodeSystem/coordinatesystem-origin"/>
  <identifier>
    <system value="urn:ietf:rfc:3986"/>
    <value value="urn:oid:2.16.840.1.113883.4.642.4.3004"/>
  </identifier>
  <version value="0.1.0-ci-build"/>
  <name value="CoordinateSystemOrigin"/>
  <title value="Coordinate System Origin CodeSystem"/>
  <status value="draft"/>
  <experimental value="true"/>
  <date value="2026-03-13"/>
  <publisher value="HL7 International / Clinical Genomics"/>
  <contact>
    <name value="HL7 International / Clinical Genomics"/>
    <telecom>
      <system value="url"/>
      <value value="http://www.hl7.org/Special/committees/clingenomics"/>
    </telecom>
    <telecom>
      <system value="email"/>
      <value value="clingenomics@lists.hl7.org"/>
    </telecom>
  </contact>
  <description
               value="The reference landmark (origin) from which coordinates are measured in a coordinateInterval. This identifies the conceptual anchor point on the molecule where numbering begins, independent of whether numbering is 0-based or 1-based (which is captured in coordinateSystem.system). No external vocabulary covers this domain-specific concept, so it is defined here by the CG Working Group."/>
  <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/cg-incubator/ValueSet/coordinatesystem-origin"/>
  <content value="complete"/>
  <concept>
    <code value="sequence-start"/>
    <display value="Sequence Start"/>
    <definition
                value="Coordinates are measured from the start of the molecule: the 5' end of a nucleotide sequence or the N-terminus of a polypeptide. This is the default for genomic, chromosomal, and transcript-level coordinate systems (e.g., NC_ or NG_ accession-based positions)."/>
  </concept>
  <concept>
    <code value="cds-start"/>
    <display value="CDS Start (A of ATG)"/>
    <definition
                value="Coordinates are measured from the adenine of the translation initiation codon (A of ATG = position 1, or 0 in 0-based systems). This is the origin used by the HGVS coding DNA reference sequence (c. prefix). Positions upstream of the ATG are negative (5' UTR); positions downstream of the stop codon are marked with an asterisk (3' UTR)."/>
  </concept>
  <concept>
    <code value="feature-start"/>
    <display value="Feature Start"/>
    <definition
                value="Coordinates are measured from the start of a named genomic feature, such as the first base of an exon. This is used for HGVS exon-relative or feature-relative position expressions."/>
  </concept>
  <concept>
    <code value="feature-end"/>
    <display value="Feature End"/>
    <definition
                value="Coordinates are measured from the end of a named genomic feature, such as the last base of an exon. A positive offset extends into the downstream intron; a negative offset extends upstream into the exon. This origin is used for HGVS intronic positions (e.g., c.100+3, where 100 is the last coding base and +3 is the offset into the intron)."/>
  </concept>
</CodeSystem>