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

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: Coordinate System Origin CodeSystem

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{
  "resourceType" : "CodeSystem",
  "id" : "coordinatesystem-origin",
  "meta" : {
    "lastUpdated" : "2026-03-13T00:00:00Z",
    "profile" : [
      🔗 "http://hl7.org/fhir/StructureDefinition/shareablecodesystem"
    ]
  },
  "language" : "en",
  "text" : {
    "status" : "generated",
    "div" : "<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>"
  },
  "extension" : [
    {
      "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
      "valueCode" : "cg"
    },
    {
      "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
      "valueCode" : "informative"
    },
    {
      "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
      "valueInteger" : 0
    }
  ],
  "url" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/coordinatesystem-origin",
  "identifier" : [
    {
      "system" : "urn:ietf:rfc:3986",
      "value" : "urn:oid:2.16.840.1.113883.4.642.4.3004"
    }
  ],
  "version" : "0.1.0-ci-build",
  "name" : "CoordinateSystemOrigin",
  "title" : "Coordinate System Origin CodeSystem",
  "status" : "draft",
  "experimental" : true,
  "date" : "2026-03-13",
  "publisher" : "HL7 International / Clinical Genomics",
  "contact" : [
    {
      "name" : "HL7 International / Clinical Genomics",
      "telecom" : [
        {
          "system" : "url",
          "value" : "http://www.hl7.org/Special/committees/clingenomics"
        },
        {
          "system" : "email",
          "value" : "clingenomics@lists.hl7.org"
        }
      ]
    }
  ],
  "description" : "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" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
          "code" : "001",
          "display" : "World"
        }
      ]
    }
  ],
  "caseSensitive" : true,
  "valueSet" : "http://hl7.org/fhir/uv/cg-incubator/ValueSet/coordinatesystem-origin",
  "content" : "complete",
  "concept" : [
    {
      "code" : "sequence-start",
      "display" : "Sequence Start",
      "definition" : "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)."
    },
    {
      "code" : "cds-start",
      "display" : "CDS Start (A of ATG)",
      "definition" : "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)."
    },
    {
      "code" : "feature-start",
      "display" : "Feature Start",
      "definition" : "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."
    },
    {
      "code" : "feature-end",
      "display" : "Feature End",
      "definition" : "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)."
    }
  ]
}