<status value="draft" /> <date value="2021-10-04" /> <publisher value="Israeli Ministry of Health" /> <description value="Proposed constraints and extensions on the Variant-Genetics Resource" /> <fhirVersion value="4.0.1" /> <mapping> <identity value="workflow" /> <uri value="http://hl7.org/fhir/workflow" /> <name value="Workflow Pattern" /> </mapping> <mapping> <identity value="sct-concept" /> <uri value="http://snomed.info/conceptdomain" /> <name value="SNOMED CT Concept Domain Binding" /> </mapping> <mapping> <identity value="v2" /> <uri value="http://hl7.org/v2" /> <name value="HL7 v2 Mapping" /> </mapping> <mapping> <identity value="rim" /> <uri value="http://hl7.org/v3" /> <name value="RIM Mapping" /> </mapping> <mapping> <identity value="w5" /> <uri value="http://hl7.org/fhir/fivews" /> <name value="FiveWs Pattern Mapping" /> </mapping> <mapping> <identity value="sct-attr" /> <uri value="http://snomed.org/attributebinding" /> <name value="SNOMED CT Attribute Binding" /> </mapping> <kind value="resource" /> <abstract value="false" /> <type value="Observation" /> <baseDefinition value="http://fhir.health.gov.il/StructureDefinition/il-core-observation" /> <derivation value="constraint" /> <differential> <element id="Observation"> <path value="Observation" /> <short value="IL Variant Genetics Profile" /> <definition value="Definitions for the profile Variant-Genetics resource profile." /> </element> <element id="Observation.identifier"> <path value="Observation.identifier" /> <slicing> <discriminator> <type value="value" /> <path value="system" /> </discriminator> <rules value="open" /> </slicing> <min value="1" /> </element> <element id="Observation.identifier.system"> <path value="Observation.identifier.system" /> <min value="1" /> <mustSupport value="true" /> </element> <element id="Observation.identifier.value"> <path value="Observation.identifier.value" /> <short value="The value that is unique within the system." /> <min value="1" /> <mustSupport value="true" /> </element> <element id="Observation.status"> <path value="Observation.status" /> <fixedCode value="final" /> </element> <element id="Observation.category"> <path value="Observation.category" /> <mustSupport value="false" /> </element> <element id="Observation.category.coding"> <path value="Observation.category.coding" /> <min value="1" /> <max value="1" /> </element> <element id="Observation.category.coding.system"> <path value="Observation.category.coding.system" /> <fixedUri value="http://terminology.hl7.org/CodeSystem/observation-category" /> </element> <element id="Observation.category.coding.code"> <path value="Observation.category.coding.code" /> <fixedCode value="laboratory" /> </element> <element id="Observation.category.coding.display"> <path value="Observation.category.coding.display" /> <fixedString value="Laboratory" /> </element> <element id="Observation.code.coding"> <path value="Observation.code.coding" /> <min value="1" /> <max value="1" /> </element> <element id="Observation.code.coding.system"> <path value="Observation.code.coding.system" /> <fixedUri value="http://loinc.org" /> </element> <element id="Observation.code.coding.code"> <path value="Observation.code.coding.code" /> <fixedCode value="69548-6" /> </element> <element id="Observation.code.coding.display"> <path value="Observation.code.coding.display" /> <fixedString value="Genetic variant assessment" /> </element> <element id="Observation.subject"> <path value="Observation.subject" /> <min value="1" /> <type> <code value="Reference" /> <targetProfile value="http://fhir.health.gov.il/StructureDefinition/il-core-patient" /> </type> </element> <element id="Observation.encounter"> <path value="Observation.encounter" /> <min value="1" /> <type> <code value="Reference" /> <targetProfile value="http://fhir.health.gov.il/StructureDefinition/il-encounter-genetics-survey" /> </type> </element> <element id="Observation.effective[x]"> <path value="Observation.effective[x]" /> <slicing> <discriminator> <type value="type" /> <path value="$this" /> </discriminator> <ordered value="false" /> <rules value="open" /> </slicing> <min value="1" /> <type> <code value="dateTime" /> </type> </element> <element id="Observation.effectiveDateTime"> <path value="Observation.effectiveDateTime" /> <min value="1" /> <max value="1" /> </element> <element id="Observation.issued"> <path value="Observation.issued" /> <min value="1" /> </element> <element id="Observation.performer"> <path value="Observation.performer" /> <type> <code value="Reference" /> <targetProfile value="http://fhir.health.gov.il/StructureDefinition/il-core-organization" /> </type> </element> <element id="Observation.value[x]"> <path value="Observation.value[x]" /> <min value="1" /> <type> <code value="CodeableConcept" /> </type> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL4034-6" /> </binding> </element> <element id="Observation.method"> <path value="Observation.method" /> <min value="1" /> <binding> <strength value="extensible" /> <valueSet value="http://loinc.org/vs/LL4048-6" /> </binding> </element> <element id="Observation.method.coding"> <path value="Observation.method.coding" /> <min value="1" /> <max value="1" /> </element> <element id="Observation.specimen"> <path value="Observation.specimen" /> <min value="1" /> <type> <code value="Reference" /> <targetProfile value="http://fhir.health.gov.il/StructureDefinition/il-specimen-genetics-survey" /> </type> </element> <element id="Observation.derivedFrom"> <path value="Observation.derivedFrom" /> <min value="1" /> <max value="1" /> <type> <code value="Reference" /> <targetProfile value="http://fhir.health.gov.il/StructureDefinition/questionnaire-response-genetics-survey" /> </type> </element> <element id="Observation.component"> <path value="Observation.component" /> <slicing> <discriminator> <type value="value" /> <path value="code.coding.system" /> </discriminator> <discriminator> <type value="value" /> <path value="code.coding.code" /> </discriminator> <rules value="open" /> </slicing> <mustSupport value="false" /> </element> <element id="Observation.component:associated-phenotype"> <path value="Observation.component" /> <sliceName value="associated-phenotype" /> <short value="Associated phenotype" /> <definition value="Associated phenotype caused by this variant." /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:associated-phenotype.code"> <path value="Observation.component.code" /> <mustSupport value="false" /> </element> <element id="Observation.component:associated-phenotype.code.coding.system"> <path value="Observation.component.code.coding.system" /> <min value="1" /> <fixedUri value="http://loinc.org" /> </element> <element id="Observation.component:associated-phenotype.code.coding.code"> <path value="Observation.component.code.coding.code" /> <min value="1" /> <fixedCode value="81259-4" /> </element> <element id="Observation.component:associated-phenotype.code.coding.display"> <path value="Observation.component.code.coding.display" /> <fixedString value="Associated phenotype" /> </element> <element id="Observation.component:associated-phenotype.value[x]"> <path value="Observation.component.value[x]" /> <short value="Codes from OMIM" /> <definition value="Changes to sequence features caused by this variant." /> <min value="1" /> <type> <code value="CodeableConcept" /> </type> <mustSupport value="false" /> <binding> <strength value="required" /> <description value="Associated Phenotype" /> <valueSet value="http://www.omim.org" /> </binding> </element> <element id="Observation.component:associated-phenotype.interpretation"> <path value="Observation.component.interpretation" /> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL604-0" /> </binding> </element> <element id="Observation.component:variant-inheritance"> <path value="Observation.component" /> <sliceName value="variant-inheritance" /> <short value="Variant Inheritance" /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:variant-inheritance.code"> <path value="Observation.component.code" /> <mustSupport value="false" /> </element> <element id="Observation.component:variant-inheritance.code.coding.system"> <path value="Observation.component.code.coding.system" /> <min value="1" /> <fixedUri value="http://loinc.org" /> </element> <element id="Observation.component:variant-inheritance.code.coding.code"> <path value="Observation.component.code.coding.code" /> <min value="1" /> <fixedCode value="79742-3" /> </element> <element id="Observation.component:variant-inheritance.code.coding.display"> <path value="Observation.component.code.coding.display" /> <fixedString value="Inheritance pattern based on family history" /> </element> <element id="Observation.component:variant-inheritance.value[x]"> <path value="Observation.component.value[x]" /> <min value="1" /> <type> <code value="CodeableConcept" /> </type> <mustSupport value="false" /> <binding> <strength value="extensible" /> <description value="Variant Inheritance (Sequence Ontology)" /> <valueSet value="http://loinc.org/vs/LL3731-8" /> </binding> </element> <element id="Observation.component:variant-inheritance.interpretation"> <path value="Observation.component.interpretation" /> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL604-0" /> </binding> </element> <element id="Observation.component:dna-chg"> <path value="Observation.component" /> <sliceName value="dna-chg" /> <short value="DNA Change - Transcript (cHGVS)" /> <definition value="Human Genome Variation Society (HGVS) nomenclature for a single DNA marker." /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:dna-chg.code"> <path value="Observation.component.code" /> <mustSupport value="false" /> </element> <element id="Observation.component:dna-chg.code.coding.system"> <path value="Observation.component.code.coding.system" /> <min value="1" /> <fixedUri value="http://loinc.org" /> </element> <element id="Observation.component:dna-chg.code.coding.code"> <path value="Observation.component.code.coding.code" /> <min value="1" /> <fixedCode value="48004-6" /> </element> <element id="Observation.component:dna-chg.code.coding.display"> <path value="Observation.component.code.coding.display" /> <fixedString value="DNA change (c.HGVS)" /> </element> <element id="Observation.component:dna-chg.value[x]"> <path value="Observation.component.value[x]" /> <min value="1" /> <type> <code value="CodeableConcept" /> </type> <mustSupport value="false" /> <binding> <strength value="required" /> <description value="HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society" /> <valueSet value="http://fhir.health.gov.il/ValueSet/hgvs-nucleotide" /> </binding> </element> <element id="Observation.component:dna-chg.interpretation"> <path value="Observation.component.interpretation" /> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL604-0" /> </binding> </element> <element id="Observation.component:dna-chg-type"> <path value="Observation.component" /> <sliceName value="dna-chg-type" /> <short value="DNA change type" /> <definition value="Codified type for associated DNA Marker. DNA Marker's use the HGVS notation which implies the DNA Marker Type, but the concurrent use of this code will allow a standard and explicit type for technical and display convenience." /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:dna-chg-type.code"> <path value="Observation.component.code" /> <mustSupport value="false" /> </element> <element id="Observation.component:dna-chg-type.code.coding.system"> <path value="Observation.component.code.coding.system" /> <min value="1" /> <fixedUri value="http://loinc.org" /> </element> <element id="Observation.component:dna-chg-type.code.coding.code"> <path value="Observation.component.code.coding.code" /> <min value="1" /> <fixedCode value="48019-4" /> </element> <element id="Observation.component:dna-chg-type.code.coding.display"> <path value="Observation.component.code.coding.display" /> <fixedString value="DNA change type" /> </element> <element id="Observation.component:dna-chg-type.value[x]"> <path value="Observation.component.value[x]" /> <short value="Concepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072)" /> <definition value="Type of DNA variation reported." /> <min value="1" /> <type> <code value="CodeableConcept" /> </type> <mustSupport value="false" /> <binding> <strength value="extensible" /> <description value="DNA Change type values (Sequence Ontology)" /> <valueSet value="http://fhir.health.gov.il/ValueSet/dna-chg-type" /> </binding> </element> <element id="Observation.component:dna-chg-type.interpretation"> <path value="Observation.component.interpretation" /> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL604-0" /> </binding> </element> <element id="Observation.component:functional-annotation"> <path value="Observation.component" /> <sliceName value="functional-annotation" /> <short value="Functional Annotation" /> <definition value="Annotated changes to sequence features caused by this variant." /> <min value="0" /> <max value="*" /> <mustSupport value="false" /> </element> <element id="Observation.component:functional-annotation.code"> <path value="Observation.component.code" /> <mustSupport value="false" /> </element> <element id="Observation.component:functional-annotation.code.coding.system"> <path value="Observation.component.code.coding.system" /> <min value="1" /> <fixedUri value="http://sequenceontology.org" /> </element> <element id="Observation.component:functional-annotation.code.coding.code"> <path value="Observation.component.code.coding.code" /> <min value="1" /> <fixedCode value="SO:0001537" /> </element> <element id="Observation.component:functional-annotation.code.coding.display"> <path value="Observation.component.code.coding.display" /> <fixedString value="A sequence variant that changes one or more structural features." /> </element> <element id="Observation.component:functional-annotation.value[x]"> <path value="Observation.component.value[x]" /> <short value="Concepts in sequence ontology under SO:0001537 (see http://www.sequenceontology.org/browser/current_release/term/SO:0001537)" /> <definition value="Changes to sequence features caused by this variant." /> <min value="1" /> <type> <code value="CodeableConcept" /> </type> <mustSupport value="false" /> <binding> <strength value="extensible" /> <description value="Functional Annotation (Sequence Ontology)" /> <valueSet value="http://fhir.health.gov.il/ValueSet/functional-annotation" /> </binding> </element> <element id="Observation.component:functional-annotation.interpretation"> <path value="Observation.component.interpretation" /> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL604-0" /> </binding> </element> <element id="Observation.component:variation-code"> <path value="Observation.component" /> <sliceName value="variation-code" /> <short value="Variation Code" /> <definition value="This term is used to report the unique identifier of the simple variant found in this study." /> <comment value="If this is present, the components can be omitted but they might be included to avoid a need to look up the information in a registry. Typically only one code would be present, though multiple codings expressing the variant in different code systems are possible." /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:variation-code.code"> <path value="Observation.component.code" /> <mustSupport value="false" /> </element> <element id="Observation.component:variation-code.code.coding.system"> <path value="Observation.component.code.coding.system" /> <min value="1" /> <fixedUri value="http://loinc.org" /> </element> <element id="Observation.component:variation-code.code.coding.code"> <path value="Observation.component.code.coding.code" /> <min value="1" /> <fixedCode value="81252-9" /> </element> <element id="Observation.component:variation-code.code.coding.display"> <path value="Observation.component.code.coding.display" /> <fixedString value="Variation Code" /> </element> <element id="Observation.component:variation-code.value[x]"> <path value="Observation.component.value[x]" /> <comment value="In valueCodebaleConcept.text field, MUST insert value from column 'Variation Location' at https://www.ncbi.nlm.nih.gov/clinvar/?term=variation-code" /> <min value="1" /> <type> <code value="CodeableConcept" /> </type> <mustSupport value="false" /> <binding> <strength value="example" /> <description value="Binding not yet defined" /> <valueSet value="http://fhir.health.gov.il/ValueSet/clinvar" /> </binding> </element> <element id="Observation.component:variation-code.value[x].text"> <path value="Observation.component.value[x].text" /> <comment value="In valueCodebaleConcept.text field, MUST insert value from column 'Variation Location' at https://www.ncbi.nlm.nih.gov/clinvar/?term=variation-code" /> <min value="1" /> </element> <element id="Observation.component:variation-code.interpretation"> <path value="Observation.component.interpretation" /> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL604-0" /> </binding> </element> <element id="Observation.component:genomic-dna-chg"> <path value="Observation.component" /> <sliceName value="genomic-dna-chg" /> <short value="DNA Change - Genomic (gHGVS)" /> <definition value="The name of a structural variant reported using HGVS nomenclature." /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:genomic-dna-chg.code"> <path value="Observation.component.code" /> <mustSupport value="false" /> </element> <element id="Observation.component:genomic-dna-chg.code.coding.system"> <path value="Observation.component.code.coding.system" /> <min value="1" /> <fixedUri value="http://loinc.org" /> </element> <element id="Observation.component:genomic-dna-chg.code.coding.code"> <path value="Observation.component.code.coding.code" /> <min value="1" /> <fixedCode value="81290-9" /> </element> <element id="Observation.component:genomic-dna-chg.code.coding.display"> <path value="Observation.component.code.coding.display" /> <fixedString value="DNA Change - Genomic (gHGVS)" /> </element> <element id="Observation.component:genomic-dna-chg.value[x]"> <path value="Observation.component.value[x]" /> <min value="1" /> <type> <code value="CodeableConcept" /> </type> <mustSupport value="false" /> <binding> <strength value="required" /> <description value="HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society" /> <valueSet value="http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs" /> </binding> </element> <element id="Observation.component:genomic-dna-chg.interpretation"> <path value="Observation.component.interpretation" /> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL604-0" /> </binding> </element> <element id="Observation.component:genomic-source-class"> <path value="Observation.component" /> <sliceName value="genomic-source-class" /> <short value="Genomic source class" /> <definition value="The genomic class of the specimen being analyzed: Germline for inherited genome, somatic for cancer genome, and prenatal for fetal genome." /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:genomic-source-class.code"> <path value="Observation.component.code" /> <mustSupport value="false" /> </element> <element id="Observation.component:genomic-source-class.code.coding.system"> <path value="Observation.component.code.coding.system" /> <min value="1" /> <fixedUri value="http://loinc.org" /> </element> <element id="Observation.component:genomic-source-class.code.coding.code"> <path value="Observation.component.code.coding.code" /> <min value="1" /> <fixedCode value="48002-0" /> </element> <element id="Observation.component:genomic-source-class.code.coding.display"> <path value="Observation.component.code.coding.display" /> <fixedString value="Genomic source class [Type]" /> </element> <element id="Observation.component:genomic-source-class.value[x]"> <path value="Observation.component.value[x]" /> <short value="Germline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo" /> <definition value="MG_2_Genetic variant source." /> <min value="1" /> <type> <code value="CodeableConcept" /> </type> <mustSupport value="false" /> <binding> <strength value="extensible" /> <description value="Genomic source class values" /> <valueSet value="http://loinc.org/vs/LL378-1" /> </binding> </element> <element id="Observation.component:genomic-source-class.interpretation"> <path value="Observation.component.interpretation" /> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL604-0" /> </binding> </element> <element id="Observation.component:amino-acid-chg"> <path value="Observation.component" /> <sliceName value="amino-acid-chg" /> <short value="Amino acid change (pHGVS)" /> <definition value="Human Genome Variation Society (HGVS) nomenclature for an amino acid sequence. This value is derivable from the DNA Marker value if available. It is provided for convenience. The use of the nomenclature must be extended to describe non-variations (aka. wild types) see samples for wild type examples." /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:amino-acid-chg.code"> <path value="Observation.component.code" /> <mustSupport value="false" /> </element> <element id="Observation.component:amino-acid-chg.code.coding.system"> <path value="Observation.component.code.coding.system" /> <min value="1" /> <fixedUri value="http://loinc.org" /> </element> <element id="Observation.component:amino-acid-chg.code.coding.code"> <path value="Observation.component.code.coding.code" /> <min value="1" /> <fixedCode value="48005-3" /> </element> <element id="Observation.component:amino-acid-chg.code.coding.display"> <path value="Observation.component.code.coding.display" /> <fixedString value="Amino acid change (pHGVS)" /> </element> <element id="Observation.component:amino-acid-chg.value[x]"> <path value="Observation.component.value[x]" /> <min value="1" /> <type> <code value="CodeableConcept" /> </type> <mustSupport value="false" /> <binding> <strength value="required" /> <description value="HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society" /> <valueSet value="http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs" /> </binding> </element> <element id="Observation.component:amino-acid-chg.interpretation"> <path value="Observation.component.interpretation" /> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL604-0" /> </binding> </element> <element id="Observation.component:amino-acid-chg-type"> <path value="Observation.component" /> <sliceName value="amino-acid-chg-type" /> <short value="Amino acid change type" /> <definition value="Codified type for associated Amino Acid Marker. Amino Acid Marker's use the HGVS notation which implies the Amino Acid Marker Type, but the concurrent use of this code will allow a standard and explicit type for technical and display convenience." /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:amino-acid-chg-type.code"> <path value="Observation.component.code" /> <mustSupport value="false" /> </element> <element id="Observation.component:amino-acid-chg-type.code.coding.system"> <path value="Observation.component.code.coding.system" /> <min value="1" /> <fixedUri value="http://loinc.org" /> </element> <element id="Observation.component:amino-acid-chg-type.code.coding.code"> <path value="Observation.component.code.coding.code" /> <min value="1" /> <fixedCode value="48006-1" /> </element> <element id="Observation.component:amino-acid-chg-type.code.coding.display"> <path value="Observation.component.code.coding.display" /> <fixedString value="Amino acid change type" /> </element> <element id="Observation.component:amino-acid-chg-type.value[x]"> <path value="Observation.component.value[x]" /> <short value="Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation" /> <definition value="MG_4_Amino acid change type." /> <min value="1" /> <type> <code value="CodeableConcept" /> </type> <mustSupport value="false" /> <binding> <strength value="required" /> <description value="Amino acid change type values" /> <valueSet value="http://loinc.org/vs/LL380-7" /> </binding> </element> <element id="Observation.component:amino-acid-chg-type.interpretation"> <path value="Observation.component.interpretation" /> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL604-0" /> </binding> </element> <element id="Observation.component:transcript-ref-seq"> <path value="Observation.component" /> <sliceName value="transcript-ref-seq" /> <short value="Transcript reference sequence ID" /> <definition value="This field carries the ID for the transcribed reference sequence, which is the part of the genomic reference sequence that is converted to messenger RNA (i.e., after the introns are removed)." /> <comment value="Only needed if the transcript sequence or genomic reference sequence versions don't indicate the version." /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:transcript-ref-seq.code"> <path value="Observation.component.code" /> <mustSupport value="false" /> </element> <element id="Observation.component:transcript-ref-seq.code.coding.system"> <path value="Observation.component.code.coding.system" /> <min value="1" /> <fixedUri value="http://loinc.org" /> </element> <element id="Observation.component:transcript-ref-seq.code.coding.code"> <path value="Observation.component.code.coding.code" /> <min value="1" /> <fixedCode value="51958-7" /> </element> <element id="Observation.component:transcript-ref-seq.code.coding.display"> <path value="Observation.component.code.coding.display" /> <fixedString value="Transcript reference sequence [ID]" /> </element> <element id="Observation.component:transcript-ref-seq.value[x]"> <path value="Observation.component.value[x]" /> <comment value="In valueCodebaleConcept.text field, MUST insert value from column 'Variation Location' at https://www.ncbi.nlm.nih.gov" /> <min value="1" /> <type> <code value="CodeableConcept" /> </type> <mustSupport value="false" /> <binding> <strength value="example" /> <description value="Binding not yet defined" /> </binding> </element> <element id="Observation.component:transcript-ref-seq.value[x].text"> <path value="Observation.component.value[x].text" /> <comment value="In valueCodebaleConcept.text field, MUST insert value from column 'Variation Location' at https://www.ncbi.nlm.nih.gov/clinvar/?term=variation-code" /> <min value="1" /> </element> <element id="Observation.component:transcript-ref-seq.interpretation"> <path value="Observation.component.interpretation" /> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL604-0" /> </binding> </element> <element id="Observation.component:genomic-ref-seq"> <path value="Observation.component" /> <sliceName value="genomic-ref-seq" /> <short value="Genomic reference sequence ID" /> <definition value="This field carries the ID for the genomic reference sequence. The genomic reference sequence is a contiguous stretch of chromosome DNA that spans all of the exons of the gene and includes transcribed and non transcribed stretches. For this ID use either the NCBI genomic nucleotide RefSeq IDs with their version number (see: NCBI.NLM.NIH.Gov/RefSeq) or use the LRG identifiers, without transcript (t or p) extensions -- when they become available. (See- Report sponsored by GEN2PHEN at the European Bioinformatics Institute at Hinxton UK April 24-25, 2008). The NCI RefSeq genomic IDs are distinguished by a prefix of"NG" for genes from the nuclear chromosomes and prefix of "NC" for genes from mitochondria. The LRG Identifiers have a prefix of "LRG_" Mitochondrial genes are not in the scope of LRG." /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:genomic-ref-seq.code"> <path value="Observation.component.code" /> <mustSupport value="false" /> </element> <element id="Observation.component:genomic-ref-seq.code.coding.system"> <path value="Observation.component.code.coding.system" /> <min value="1" /> <fixedUri value="http://loinc.org" /> </element> <element id="Observation.component:genomic-ref-seq.code.coding.code"> <path value="Observation.component.code.coding.code" /> <min value="1" /> <fixedCode value="48013-7" /> </element> <element id="Observation.component:genomic-ref-seq.code.coding.display"> <path value="Observation.component.code.coding.display" /> <fixedString value="Genomic reference sequence [ID]" /> </element> <element id="Observation.component:genomic-ref-seq.value[x]"> <path value="Observation.component.value[x]" /> <comment value="In valueCodebaleConcept.text field, MUST insert value from https://www.ncbi.nlm.nih.gov" /> <min value="1" /> <type> <code value="CodeableConcept" /> </type> <mustSupport value="false" /> <binding> <strength value="example" /> <description value="Binding not yet defined" /> </binding> </element> <element id="Observation.component:genomic-ref-seq.value[x].text"> <path value="Observation.component.value[x].text" /> <min value="1" /> </element> <element id="Observation.component:genomic-ref-seq.interpretation"> <path value="Observation.component.interpretation" /> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL604-0" /> </binding> </element> <element id="Observation.component:allelic-state"> <path value="Observation.component" /> <sliceName value="allelic-state" /> <short value="Allelic state" /> <definition value="The level of occurrence of a single DNA Marker within a set of chromosomes. Heterozygous indicates the DNA Marker is only present in one of the two genes contained in homologous chromosomes. Homozygous indicates the DNA Marker is present in both genes contained in homologous chromosomes. Hemizygous indicates the DNA Marker exists in the only single copy of a gene in a non-homologous chromosome (The male X and Y chromosome are non-homologous). Hemiplasmic indicates that the DNA Marker is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA Maker is present in all of the copies of mitochondrial DNA." /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:allelic-state.code"> <path value="Observation.component.code" /> <mustSupport value="false" /> </element> <element id="Observation.component:allelic-state.code.coding.system"> <path value="Observation.component.code.coding.system" /> <min value="1" /> <fixedUri value="http://loinc.org" /> </element> <element id="Observation.component:allelic-state.code.coding.code"> <path value="Observation.component.code.coding.code" /> <min value="1" /> <fixedCode value="53034-5" /> </element> <element id="Observation.component:allelic-state.code.coding.display"> <path value="Observation.component.code.coding.display" /> <fixedString value="Allelic state" /> </element> <element id="Observation.component:allelic-state.value[x]"> <path value="Observation.component.value[x]" /> <short value="Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous" /> <definition value="The relationship between the alleles found at the same locus on different chromosomes." /> <min value="1" /> <type> <code value="CodeableConcept" /> </type> <mustSupport value="false" /> <binding> <strength value="extensible" /> <description value="Allelic state type values" /> <valueSet value="http://loinc.org/vs/LL381-5" /> </binding> </element> <element id="Observation.component:allelic-state.interpretation"> <path value="Observation.component.interpretation" /> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL604-0" /> </binding> </element> <element id="Observation.component:copy-number"> <path value="Observation.component" /> <sliceName value="copy-number" /> <short value="Genomic structural variant copy number" /> <definition value="The copy number of the large variant. In HGVS, this is the numeric value following the “X”. It is a unit-less value. Note that a copy number of 1 implies a deletion. The copy number can usually be inferred from the HGVS or ISCN fields." /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:copy-number.code"> <path value="Observation.component.code" /> <mustSupport value="false" /> </element> <element id="Observation.component:copy-number.code.coding.system"> <path value="Observation.component.code.coding.system" /> <min value="1" /> <fixedUri value="http://loinc.org" /> </element> <element id="Observation.component:copy-number.code.coding.code"> <path value="Observation.component.code.coding.code" /> <min value="1" /> <fixedCode value="82155-3" /> </element> <element id="Observation.component:copy-number.code.coding.display"> <path value="Observation.component.code.coding.display" /> <fixedString value="Genomic structural variant copy number" /> </element> <element id="Observation.component:copy-number.value[x]"> <path value="Observation.component.value[x]" /> <min value="1" /> <type> <code value="Quantity" /> <profile value="http://hl7.org/fhir/StructureDefinition/SimpleQuantity" /> </type> <mustSupport value="false" /> </element> <element id="Observation.component:copy-number.interpretation"> <path value="Observation.component.interpretation" /> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL604-0" /> </binding> </element> <element id="Observation.component:ref-allele"> <path value="Observation.component" /> <sliceName value="ref-allele" /> <short value="Genomic ref allele" /> <definition value="Reference values ("normal") examined within the Reference Sequence." /> <comment value="This is used in a genotyping test to define the reference and variable nucleotide strings. That is if the sequence variation is an insertion, then Reference Nucleotide will be blank and Variable Nucleotide will contain the inserted nucleotides. In contrast, if the sequence variation is a deletion, then the Reference Nucleotide will contain the deleted nucliotieds, and the Variable Nucleotide will be blank." /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:ref-allele.code"> <path value="Observation.component.code" /> <mustSupport value="false" /> </element> <element id="Observation.component:ref-allele.code.coding.system"> <path value="Observation.component.code.coding.system" /> <min value="1" /> <fixedUri value="http://loinc.org" /> </element> <element id="Observation.component:ref-allele.code.coding.code"> <path value="Observation.component.code.coding.code" /> <min value="1" /> <fixedCode value="69547-8" /> </element> <element id="Observation.component:ref-allele.code.coding.display"> <path value="Observation.component.code.coding.display" /> <fixedString value="Genomic ref allele [ID]" /> </element> <element id="Observation.component:ref-allele.value[x]"> <path value="Observation.component.value[x]" /> <min value="1" /> <type> <code value="string" /> </type> <mustSupport value="false" /> </element> <element id="Observation.component:ref-allele.interpretation"> <path value="Observation.component.interpretation" /> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL604-0" /> </binding> </element> <element id="Observation.component:alt-allele"> <path value="Observation.component" /> <sliceName value="alt-allele" /> <short value="Genomic alt allele" /> <definition value="The genomic alternate allele is the contiguous segment of DNA in the test sample that differs from the reference allele at the same location and thus defines a variant." /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:alt-allele.code"> <path value="Observation.component.code" /> <mustSupport value="false" /> </element> <element id="Observation.component:alt-allele.code.coding.system"> <path value="Observation.component.code.coding.system" /> <min value="1" /> <fixedUri value="http://loinc.org" /> </element> <element id="Observation.component:alt-allele.code.coding.code"> <path value="Observation.component.code.coding.code" /> <min value="1" /> <fixedCode value="69551-0" /> </element> <element id="Observation.component:alt-allele.code.coding.display"> <path value="Observation.component.code.coding.display" /> <fixedString value="Genomic alt allele [ID]" /> </element> <element id="Observation.component:alt-allele.value[x]"> <path value="Observation.component.value[x]" /> <min value="1" /> <type> <code value="string" /> </type> <mustSupport value="false" /> </element> <element id="Observation.component:alt-allele.interpretation"> <path value="Observation.component.interpretation" /> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL604-0" /> </binding> </element> <element id="Observation.component:coordinate-system"> <path value="Observation.component" /> <sliceName value="coordinate-system" /> <short value="Coordinate System" /> <definition value="Base number of coordinate system either 0-based, with inclusive start and exclusive end (called interval), or 1-based, with inclusive start and end. However, two versions of 1-based are in common use.These systems are HGVS 1-based (called variant method) and VCF 1-based (called alignment method). In general, HGVS recommends right-justification and VCF recommends left-justification. However, these systems further address questions such as wheather or not to place an insertion before or after the nucleotide, and, if always placed before the nucleotide, how to handle insertion after the end of the sequence. Additionally, the systems deal with handling boundary effects of numbers between features. For more details see the HGVS and VCF guides." /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:coordinate-system.code"> <path value="Observation.component.code" /> <definition value="This captures the base numbering used to calculate base positions in the reported sequence information." /> <mustSupport value="false" /> </element> <element id="Observation.component:coordinate-system.code.coding.system"> <path value="Observation.component.code.coding.system" /> <min value="1" /> <fixedUri value="http://loinc.org" /> </element> <element id="Observation.component:coordinate-system.code.coding.code"> <path value="Observation.component.code.coding.code" /> <min value="1" /> <fixedCode value="92822-6" /> </element> <element id="Observation.component:coordinate-system.code.coding.display"> <path value="Observation.component.code.coding.display" /> <fixedString value="Genomic coordinate system [Type]" /> </element> <element id="Observation.component:coordinate-system.value[x]"> <path value="Observation.component.value[x]" /> <short value="0-based interval | 0-based character | 1-based character" /> <min value="1" /> <type> <code value="CodeableConcept" /> </type> <mustSupport value="false" /> <binding> <strength value="preferred" /> <description value="Base coordinate systems start and end measurements for variants" /> <valueSet value="http://loinc.org/vs/LL5323-2" /> </binding> </element> <element id="Observation.component:coordinate-system.interpretation"> <path value="Observation.component.interpretation" /> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL604-0" /> </binding> </element> <element id="Observation.component:exact-start-end"> <path value="Observation.component" /> <sliceName value="exact-start-end" /> <short value="Exact start-end" /> <definition value="This location is the first genomic position in the reference allele that contains a change from the reference allele. For example, for the simple variant NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys), the location is Chr3: 128906220 on Assembly GRCh38." /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:exact-start-end.code"> <path value="Observation.component.code" /> <mustSupport value="false" /> </element> <element id="Observation.component:exact-start-end.code.coding.system"> <path value="Observation.component.code.coding.system" /> <min value="1" /> <fixedUri value="http://loinc.org" /> </element> <element id="Observation.component:exact-start-end.code.coding.code"> <path value="Observation.component.code.coding.code" /> <min value="1" /> <fixedCode value="LP212296-0" /> </element> <element id="Observation.component:exact-start-end.code.coding.display"> <path value="Observation.component.code.coding.display" /> <fixedString value="Variant exact start-end" /> </element> <element id="Observation.component:exact-start-end.value[x]"> <path value="Observation.component.value[x]" /> <min value="1" /> <type> <code value="Range" /> </type> <mustSupport value="false" /> </element> <element id="Observation.component:exact-start-end.value[x].low"> <path value="Observation.component.value[x].low" /> <short value="Exact Start" /> <min value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:exact-start-end.value[x].high"> <path value="Observation.component.value[x].high" /> <short value="Exact End" /> <definition value="Optional since many representations (VCF, SPDI) only provide a single position." /> <mustSupport value="false" /> </element> <element id="Observation.component:exact-start-end.interpretation"> <path value="Observation.component.interpretation" /> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL604-0" /> </binding> </element> <element id="Observation.component:variant-length"> <path value="Observation.component" /> <sliceName value="variant-length" /> <short value="Structural variant length" /> <definition value="Length of the structural variant, which information may be ascertained in some but not all types of structural variants." /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:variant-length.code"> <path value="Observation.component.code" /> <mustSupport value="false" /> </element> <element id="Observation.component:variant-length.code.coding.system"> <path value="Observation.component.code.coding.system" /> <min value="1" /> <fixedUri value="http://loinc.org" /> </element> <element id="Observation.component:variant-length.code.coding.code"> <path value="Observation.component.code.coding.code" /> <min value="1" /> <fixedCode value="81300-6" /> </element> <element id="Observation.component:variant-length.code.coding.display"> <path value="Observation.component.code.coding.display" /> <fixedString value="Structural variant [Length]" /> </element> <element id="Observation.component:variant-length.value[x]"> <path value="Observation.component.value[x]" /> <min value="1" /> <type> <code value="Quantity" /> <profile value="http://hl7.org/fhir/StructureDefinition/SimpleQuantity" /> </type> <mustSupport value="false" /> </element> <element id="Observation.component:variant-length.interpretation"> <path value="Observation.component.interpretation" /> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL604-0" /> </binding> </element> <element id="Observation.component:chromosome-copy-number-change-type"> <path value="Observation.component" /> <sliceName value="chromosome-copy-number-change-type" /> <short value="Chromosome copy number change type" /> <definition value="The type of the chromosome copy number change." /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:chromosome-copy-number-change-type.code"> <path value="Observation.component.code" /> <mustSupport value="false" /> </element> <element id="Observation.component:chromosome-copy-number-change-type.code.coding.system"> <path value="Observation.component.code.coding.system" /> <min value="1" /> <fixedUri value="http://loinc.org" /> </element> <element id="Observation.component:chromosome-copy-number-change-type.code.coding.code"> <path value="Observation.component.code.coding.code" /> <min value="1" /> <fixedCode value="62378-5" /> </element> <element id="Observation.component:chromosome-copy-number-change-type.code.coding.display"> <path value="Observation.component.code.coding.display" /> <fixedString value="Chromosome copy number change [Type]" /> </element> <element id="Observation.component:chromosome-copy-number-change-type.value[x]"> <path value="Observation.component.value[x]" /> <short value="Copy number gain | Copy number loss" /> <min value="1" /> <type> <code value="CodeableConcept" /> </type> <mustSupport value="false" /> <binding> <strength value="required" /> <description value="Copy Number Change Types" /> <valueSet value="http://loinc.org/vs/LL1041-4" /> </binding> </element> <element id="Observation.component:chromosome-copy-number-change-type.interpretation"> <path value="Observation.component.interpretation" /> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL604-0" /> </binding> </element> <element id="Observation.component:arrCGH-ratio"> <path value="Observation.component" /> <sliceName value="arrCGH-ratio" /> <short value="Structural variant reported arrCGH [Ratio]" /> <definition value="arrCGH ratio" /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:arrCGH-ratio.code"> <path value="Observation.component.code" /> <mustSupport value="false" /> </element> <element id="Observation.component:arrCGH-ratio.code.coding.system"> <path value="Observation.component.code.coding.system" /> <min value="1" /> <fixedUri value="http://loinc.org" /> </element> <element id="Observation.component:arrCGH-ratio.code.coding.code"> <path value="Observation.component.code.coding.code" /> <min value="1" /> <fixedCode value="81299-0" /> </element> <element id="Observation.component:arrCGH-ratio.code.coding.display"> <path value="Observation.component.code.coding.display" /> <fixedString value="Structural variant reported arrCGH [Ratio]" /> </element> <element id="Observation.component:arrCGH-ratio.value[x]"> <path value="Observation.component.value[x]" /> <min value="1" /> <type> <code value="Quantity" /> <profile value="http://hl7.org/fhir/StructureDefinition/SimpleQuantity" /> </type> <mustSupport value="false" /> </element> <element id="Observation.component:arrCGH-ratio.interpretation"> <path value="Observation.component.interpretation" /> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL604-0" /> </binding> </element> <element id="Observation.component:complex-var-type"> <path value="Observation.component" /> <sliceName value="complex-var-type" /> <short value="Complex variant type" /> <definition value="The type of complex variant, for example, compound heterozygous or haplotype." /> <comment value="When sending a grouping of non-contiguous variants that are meant to be interpreted together but do not signify a named haplotype, one can send the type of complex variant here (determined by where the individual changes are in relation to each other), and use Observation.hasMember to reference the individual variants, which would then be described as normal." /> <min value="0" /> <max value="1" /> <mustSupport value="false" /> </element> <element id="Observation.component:complex-var-type.code"> <path value="Observation.component.code" /> <mustSupport value="false" /> </element> <element id="Observation.component:complex-var-type.code.coding.system"> <path value="Observation.component.code.coding.system" /> <min value="1" /> <fixedUri value="http://loinc.org" /> </element> <element id="Observation.component:complex-var-type.code.coding.code"> <path value="Observation.component.code.coding.code" /> <min value="1" /> <fixedCode value="81263-6" /> </element> <element id="Observation.component:complex-var-type.code.coding.display"> <path value="Observation.component.code.coding.display" /> <fixedString value="Complex variant type" /> </element> <element id="Observation.component:complex-var-type.value[x]"> <path value="Observation.component.value[x]" /> <short value="Compound heterozygous | Double heterozygous | Haplotype | Hemizygous" /> <min value="1" /> <type> <code value="CodeableConcept" /> </type> <mustSupport value="false" /> <binding> <strength value="required" /> <description value="Complex variant type" /> <valueSet value="http://loinc.org/vs/LL3999-1" /> </binding> </element> <element id="Observation.component:complex-var-type.interpretation"> <path value="Observation.component.interpretation" /> <binding> <strength value="required" /> <valueSet value="http://loinc.org/vs/LL604-0" /> </binding> </element> </differential> </StructureDefinition>