{ "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" : "

Generated Narrative: CodeSystem coordinatesystem-origin

Last updated: 2026-03-13 00:00:00+0000

Profile: Shareable CodeSystem

This case-sensitive code system http://hl7.org/fhir/uv/cg-incubator/CodeSystem/coordinatesystem-origin defines the following codes:

CodeDisplayDefinition
sequence-start Sequence StartCoordinates 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).
cds-start CDS Start (A of ATG)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).
feature-start Feature StartCoordinates 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.
feature-end Feature EndCoordinates 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).
" }, "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)." }] }