Generated Narrative: StructureDefinition ext-R4B-MolecularSequence.variant Name Flags Card. Type Description & Constraints <a href="StructureDefinition-ext-R4B-MolecularSequence.variant-definitions.html#Extension" title="The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string.">Extension 0..* Extension(5.0.0) Variant in sequence #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Closed by value:url #xD; extension:start 0..1 Extension Start position of the variant on the reference sequence #xD; url 1..1 uri "start" #xD; value[x] 0..1 integer Start position of the variant on the reference sequence #xD; extension:end 0..1 Extension End position of the variant on the reference sequence #xD; url 1..1 uri "end" #xD; value[x] 0..1 integer End position of the variant on the reference sequence #xD; <a href="StructureDefinition-ext-R4B-MolecularSequence.variant-definitions.html#Extension.extension:observedAllele" title="Slice observedAllele: An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.">extension:observedAllele 0..1 Extension Allele that was observed #xD; url 1..1 uri "observedAllele" #xD; <a href="StructureDefinition-ext-R4B-MolecularSequence.variant-definitions.html#Extension.extension:observedAllele.value[x]" title="An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.">value[x] 0..1 string Allele that was observed #xD; <a href="StructureDefinition-ext-R4B-MolecularSequence.variant-definitions.html#Extension.extension:referenceAllele" title="Slice referenceAllele: An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.">extension:referenceAllele 0..1 Extension Allele in the reference sequence #xD; url 1..1 uri "referenceAllele" #xD; <a href="StructureDefinition-ext-R4B-MolecularSequence.variant-definitions.html#Extension.extension:referenceAllele.value[x]" title="An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.">value[x] 0..1 string Allele in the reference sequence #xD; extension:cigar 0..1 Extension Extended CIGAR string for aligning the sequence with reference bases #xD; url 1..1 uri "cigar" #xD; value[x] 0..1 string Extended CIGAR string for aligning the sequence with reference bases #xD; extension:variantPointer 0..1 Extension Pointer to observed variant information #xD; url 1..1 uri "variantPointer" #xD; value[x] 0..1 Reference() Pointer to observed variant information #xD; url 1..1 uri "http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.variant" #xD; Documentation for this format
Cross-version Extension for R4B.MolecularSequence.variant for use in FHIR R5
This cross-version extension represents MolecularSequence.variant from http://hl7.org/fhir/StructureDefinition/MolecularSequence|4.3.0 for use in FHIR R5.
The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string.
`MolecularSequence.variant` has no related element in R5:MolecularSequence
All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
Must have either extensions or value[x], not both
Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Extensions are always sliced by (at least) url
Start position of the variant on the reference sequence
Start position of the variant on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
Additional content defined by implementations
May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and managable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.
There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
Source of the definition for the extension code - a logical name or a URL.
The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
End position of the variant on the reference sequence
End position of the variant on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.
An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.
An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.
Extended CIGAR string for aligning the sequence with reference bases
Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).
A pointer to an Observation containing variant information.
Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/R5/extensibility.html) for a list).