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Questionnaire: Reportable Variant Result Panel

Official URL: https://fhir.nwgenomics.nhs.uk/Questionnaire/ReportableVariantResultPanel Version: 2.2.0
Draft as of 2026-09-20 Computable Name:

Result panel for a Variant (Reportable Variant) Observation, structured around the HL7 v2 Lab Results Interface (LRI)'s own Discrete Variant Panel (LOINC 81250-3, LRI Chapter 5 Table 5-2, plus the Structural Variant Addenda in Table 5-3) - the same panel the NTHL1 and CFTR examples are based on. LRI already defines this as a single panel covering both simple and structural variants; this Questionnaire follows that same single-panel structure rather than iGene's separate per-variant-type field sets, mapping each item to both its LRI OBX row and its corresponding component in the HL7 Genomics Reporting IG's Variant profile. See OMICS DSS Result Integration for the full LRI/FHIR/iGene three-way mapping table.

item.definition/item.code are cross-checked against this IG's current Variant examples: Variant - NTHL1 and Variant - CFTR (both based on LRI examples), Observation-EGFR-Variant-ctDNA, Observation-BRCA1, and the four Variant Observations (a small variant, an intragenic CNV, a multi-gene CNV and a structural variant) in Bundle-ctdna9737383222-testresults, plus iGene's own custom field spec for variants (NotGit/iGene Custom Fields Master Dataset - Updated 13-Aug-26.xlsx, "Variant Level Data" sheet) - only elements genuinely populated by at least one of these is modelled, since these are the only elements needed for the iGene feed. See OMICS DSS Result Integration - Result Panel: Elements Not Included for the LRI/FHIR elements deliberately left out because no current example populates them.

Known gaps between iGene, LRI and the FHIR profile, not yet resolved:

  • Loss of Heterozygosity is one of iGene's five variant types, but has no corresponding row anywhere in LRI's Discrete Variant Panel - LRI's closest concept, Allelic State (53034-5, row B.23), does not offer an LOH answer option. No current FHIR example produces LOH data either.
  • Coordinate System [Type] (92822-6) and Origin of Germline Genetic Variant [Type] (94186-4), both used by the ctDNA Bundle examples, have no row in LRI's Discrete Variant Panel - LRI's closest concept to the latter is Allelic Phase (82120-7, row B.26), a different LOINC code whose answer list happens to include Maternal/Paternal as two of several "sets of variants in cis" options, not a dedicated parent-of-origin field.
  • Structural Variant: iGene expects a single Complex variant HGVS name field (LOINC 81262-8 - itself an LRI Complex Variant Panel code, row C.2, not part of the Discrete Variant Panel at all), but the ctDNA Bundle's structural-variant Observation does not populate 81262-8 - it uses several Discrete Variant Panel components instead (Genomic Reference Sequence, Coordinate System, Genomic Ref/Alt Allele, DNA Change Type, Genomic DNA Change).

Profile: Questionnaire

LinkIDTextCardinalityTypeDescription & Constraintsdoco
.. Result panel for a [Variant (Reportable Variant)](StructureDefinition-Variant.html) `Observation`, structured around the HL7 v2 [Lab Results Interface (LRI)](https://confluence.hl7.org/download/attachments/25559919/2018%2004%2003%20-%20V2%20LRI%20-%20Ch.%205%20CG%20and%20Code%20System%20Tables.pdf?api=v2)'s own **Discrete Variant Panel** (LOINC `81250-3`, LRI Chapter 5 Table 5-2, plus the Structural Variant Addenda in Table 5-3) - the same panel the NTHL1 and CFTR examples are based on. LRI already defines this as a single panel covering both simple and structural variants; this Questionnaire follows that same single-panel structure rather than iGene's separate per-variant-type field sets, mapping each item to both its LRI `OBX` row and its corresponding component in the HL7 Genomics Reporting IG's [Variant](https://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-variant.html) profile. See [OMICS DSS Result Integration](reportable-variants.html) for the full LRI/FHIR/iGene three-way mapping table. `item.definition`/`item.code` are cross-checked against this IG's current `Variant` examples: [Variant - NTHL1](Observation-8385c2fd-313d-4fd5-b98e-d5ea4bae6f99.html) and [Variant - CFTR](Observation-bca547c1-78a5-41be-8cfc-03c05805ac85.html) (both based on LRI examples), `Observation-EGFR-Variant-ctDNA`, `Observation-BRCA1`, and the four `Variant` Observations (a small variant, an intragenic CNV, a multi-gene CNV and a structural variant) in [Bundle-ctdna9737383222-testresults](Bundle-ctdna9737383222-testresults.html), plus iGene's own custom field spec for variants (`NotGit/iGene Custom Fields Master Dataset - Updated 13-Aug-26.xlsx`, "Variant Level Data" sheet) - only elements genuinely populated by at least one of these is modelled, since these are the only elements needed for the iGene feed. See [OMICS DSS Result Integration - Result Panel: Elements Not Included](reportable-variants.html#result-panel-elements-not-included) for the LRI/FHIR elements deliberately left out because no current example populates them. **Known gaps between iGene, LRI and the FHIR profile, not yet resolved:** - **Loss of Heterozygosity** is one of iGene's five variant types, but has **no corresponding row anywhere in LRI's Discrete Variant Panel** - LRI's closest concept, Allelic State (`53034-5`, row B.23), does not offer an LOH answer option. No current FHIR example produces LOH data either. - **Coordinate System [Type]** (`92822-6`) and **Origin of Germline Genetic Variant [Type]** (`94186-4`), both used by the ctDNA Bundle examples, have **no row in LRI's Discrete Variant Panel** - LRI's closest concept to the latter is Allelic Phase (`82120-7`, row B.26), a different LOINC code whose answer list happens to include Maternal/Paternal as two of several "sets of variants in cis" options, not a dedicated parent-of-origin field. - **Structural Variant**: iGene expects a single `Complex variant HGVS name` field (LOINC `81262-8` - itself an LRI Complex Variant Panel code, row C.2, not part of the Discrete Variant Panel at all), but the ctDNA Bundle's structural-variant Observation does not populate `81262-8` - it uses several Discrete Variant Panel components instead (Genomic Reference Sequence, Coordinate System, Genomic Ref/Alt Allele, DNA Change Type, Genomic DNA Change). Questionnaire https://fhir.nwgenomics.nhs.uk/Questionnaire/ReportableVariantResultPanel#2.2.0
... DiscreteVariantPanel Discrete Variant Panel 0..* group Definition: Observation
Value Set:
.... DiscreteVariantPanel-designNote LRI Table 5-2 row B - repeats for each discrete variant reported (OBX-4 sub-ID "2a", incrementing per repeat). 0..1 display Value Set:
.... LRI/B.1 Variant Category 0..1 choice Definition: Observation.component.valueCodeableConcept
Value Set:
..... LRI/B.1-designNote LRI row B.1, OBX type CWE, R/O/C = O, [0..1]. LRI's own answer list (LL4165-8) only distinguishes Simple Variant vs Structural Variant - not granular enough to route a variant to the correct iGene slot type. Resolved: this IG binds this component to its own [IGeneVariantCategory](CodeSystem-IGeneVariantCategory.html) value set instead (`SEQV`/`ICNV`/`MCNV`/`SV`/`LOH`), making the classification that used to be inferred (see [OMICS DSS Result Integration](reportable-variants.html#outstanding-issues)) an explicit, coded value - the FHIR Variant profile has no named slice for this at all, so it is modelled here as an open-slice component, same as `Variant.component:variant-category`. Populated by every current example. 0..1 display Value Set:
.... TranscriptSpecification Transcript Specification 0..1 group Definition: Observation.component
Value Set:
..... LRI/B.3 Gene Studied 0..1 choice Definition: Observation.component.valueCodeableConcept
Value Set:
...... LRI/B.3-designNote LRI row B.3, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile: this IG's own `gene-studied` addition (not one of the international profile's named slices). iGene: rolled into the free-text Description field (SEQV/ICNV) or the Gene(s) field (LOH). Used by NTHL1, CFTR, EGFR-ctDNA, and the ctDNA Bundle's small-variant and intragenic-CNV Observations. 0..1 display Value Set:
..... LRI/B.4 Transcript Reference Sequence 0..1 choice Definition: Observation.component.valueCodeableConcept
Value Set:
...... LRI/B.4-designNote LRI row B.4, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice: `representative-transcript-ref-seq`. iGene: rolled into the free-text Description field (SEQV/ICNV). Used by NTHL1, CFTR and the ctDNA Bundle's small-variant Observation. 0..1 display Value Set:
..... LRI/B.5 DNA Change (c.HGVS) 0..1 choice Definition: Observation.component.valueCodeableConcept
Value Set:
...... LRI/B.5-designNote LRI row B.5, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice: `representative-coding-hgvs`. iGene: rolled into the free-text Description field (SEQV/ICNV). Used by EGFR-ctDNA, BRCA1 and the ctDNA Bundle's small-variant Observation. 0..1 display Value Set:
..... LRI/B.6 Amino Acid Change (pHGVS) 0..1 choice Definition: Observation.component.valueCodeableConcept
Value Set:
...... LRI/B.6-designNote LRI row B.6, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice: `representative-protein-hgvs`. iGene: rolled into the free-text Description field (SEQV only - ICNV's Description omits this). Used only by the ctDNA Bundle's small-variant Observation. 0..1 display Value Set:
..... LRI/B.7 DNA Change Type 0..1 choice Definition: Observation.component.valueCodeableConcept
Value Set:
...... LRI/B.7-designNote LRI row B.7, OBX type CWE, R/O/C = O, [0..1]. FHIR Variant profile slice: `coding-change-type`. Not a discrete iGene field - summarised within iGene's free-text Description/Genomic_coordinates fields. Used by every current example (Sequence Ontology or LOINC answer coding, e.g. duplication, deletion, substitution, copy_number_variation). 0..1 display Value Set:
.... GenomicSpecification Genomic Specification 0..1 group Definition: Observation.component
Value Set:
..... LRI/B.9 Genomic Reference Sequence 0..1 choice Definition: Observation.component.valueCodeableConcept
Value Set:
...... LRI/B.9-designNote LRI row B.9, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice: `genomic-ref-seq`. iGene: rolled into the free-text Genomic_coordinates field (all four variant types). Used by NTHL1 and all four ctDNA Bundle Observations. 0..1 display Value Set:
..... LRI/B.10 Genomic DNA Change (gHGVS) 0..1 choice Definition: Observation.component.valueCodeableConcept
Value Set:
...... LRI/B.10-designNote LRI row B.10, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice: `genomic-hgvs`. iGene: rolled into the free-text Genomic_coordinates field (all four variant types). Used by all four ctDNA Bundle Observations - not by NTHL1/CFTR, where it is commented out pending a confirmed mapping. 0..1 display Value Set:
..... LRI/B.11 Genomic Ref Allele 0..1 string Definition: Observation.component.valueString
Value Set:
...... LRI/B.11-designNote LRI row B.11, OBX type ST, R/O/C = C, [0..1]. FHIR Variant profile slice: `ref-allele`. Not a discrete iGene field - summarised within iGene's Genomic_coordinates field. Used by NTHL1, CFTR and all four ctDNA Bundle Observations. 0..1 display Value Set:
..... LRI/B.12 Genomic Allele Start-End 0..1 string Definition: Observation.component.valueRange
Value Set:
...... LRI/B.12-designNote LRI row B.12, OBX type NR, R/O/C = C, [0..1]. FHIR Variant profile slice: `exact-start-end`. Not a discrete iGene field. Used only by the ctDNA Bundle's small-variant Observation - a Range with only the low bound populated. 0..1 display Value Set:
..... LRI/B.13 Genomic Alt Allele 0..1 string Definition: Observation.component.valueString
Value Set:
...... LRI/B.13-designNote LRI row B.13, OBX type ST, R/O/C = C, [0..1]. FHIR Variant profile slice: `alt-allele`. Not a discrete iGene field - summarised within iGene's Genomic_coordinates field. Used by the ctDNA Bundle's intragenic-CNV, multi-gene-CNV and structural-variant Observations (as symbolic ALT alleles, e.g. "<DEL>") - not by the small-variant Observation, NTHL1 or CFTR. 0..1 display Value Set:
.... OtherAttributes Other Attributes 0..1 group Definition: Observation.component
Value Set:
..... LRI/B.17 Cytogenetic (Chromosome) Location 0..1 string Definition: Observation.component.valueCodeableConcept
Value Set:
...... LRI/B.17-designNote LRI row B.17, OBX type CWE, R/O/C = O, [0..1]. Not one of the international FHIR Variant profile's named component slices (its closest named slice, Cytogenomic Nomenclature 81291-7, is actually a different LRI field - Table 5-1 row A.11, part of the report-level Master Panel, not this Discrete Variant Panel) - captured here as an open-slice addition, consistent with GenomicObservation's open component slicing. iGene: this is the sole field for the Multigenic CNV Description, and part of the Genomic_coordinates field for the other three variant types. Used only by the ctDNA Bundle's multi-gene-CNV Observation (e.g. "Xq22.1-q28"). 0..1 display Value Set:
..... LRI/B.18 Genomic Source Class 0..1 choice Definition: Observation.component.valueCodeableConcept
Value Set:
...... LRI/B.18-designNote LRI row B.18, OBX type CNE, R/O/C = R (required when present), [0..*]. FHIR Variant profile slice: `genomic-source-class`. Not a discrete iGene field. Used by NTHL1, CFTR, EGFR-ctDNA and the ctDNA Bundle's small-variant, intragenic-CNV and multi-gene-CNV Observations (Germline or Somatic) - not by the structural-variant Observation. 0..1 display Value Set:
.... Interpretations Interpretations 0..1 group Definition: Observation.component
Value Set:
..... LRI/B.20 Classification 0..1 choice Definition: Observation.component.valueCodeableConcept
Value Set:
...... LRI/B.20-designNote LRI row B.20 (LRI names it "Genetic sequence variation clinical significance"), OBX type CNE, R/O/C = O, [0..1]. FHIR Variant profile: not one of the profile's own component slices (the profile relies on the generic `Observation.interpretation`/`valueCodeableConcept` pattern for this) - modelled here as an open-slice component to match how every current example actually carries it. iGene: this is the Classification field for all four variant types. Used by all four ctDNA Bundle Observations (e.g. "Pathogenic"). 0..1 display Value Set:
.... AllelicStatePhase Allelic State/Phase Information 0..1 group Definition: Observation.component
Value Set:
..... LRI/B.23 Allelic State 0..1 choice Definition: Observation.component.valueCodeableConcept
Value Set:
...... LRI/B.23-designNote LRI row B.23, OBX type CNE, R/O/C = C, [0..1], answer list LL381-5 (Heteroplasmic/Homoplasmic/Homozygous/Heterozygous/Hemizygous - no "Loss of Heterozygosity" option). FHIR Variant profile slice: `allelic-state`. iGene: the Zygosity/Copy-number state field for all five variant types (iGene's LOH "State" field has no LOINC code and is a different concept - LRI has no LOH answer here). Used by NTHL1, CFTR, BRCA1 and the ctDNA Bundle's small-variant Observation (Heterozygous). 0..1 display Value Set:
..... LRI/B.24 Allelic Frequency 0..1 decimal Definition: Observation.component.valueQuantity
Value Set:
...... LRI/B.24-designNote LRI row B.24 (LRI names it "Allelic Frequency [NFr]", the FHIR profile and our examples call it "Sample variant allelic frequency [NFr]" - same LOINC code, slightly different display text), OBX type NM, R/O/C = C, [0..1]. FHIR Variant profile slice: `sample-allelic-frequency`. iGene: the Level (VAF %) field for the four variant types that have one (not LOH). Used by EGFR-ctDNA (as a percentage) and all four ctDNA Bundle Observations (as a decimal fraction) - the units differ between the two sources. 0..1 display Value Set:
.... StructuralVariantAddenda Structural Variant Addenda 0..1 group Definition: Observation.component
Value Set:
..... StructuralVariantAddenda-designNote LRI Table 5-3 - part of the same Discrete Variant Panel in the HL7 v2 message, shown as a separate table in LRI purely for visual separation of structural-variant-only attributes. 0..1 display Value Set:
..... LRI/B.28 Genomic Structural Variant Copy Number 0..1 decimal Definition: Observation.component.valueQuantity
Value Set:
...... LRI/B.28-designNote LRI row B.28, OBX type NM, R/O/C = O, [0..1], OBX-4 sub-ID "2a.1". FHIR Variant profile slice: `copy-number`. Not a discrete iGene field - the closest iGene concept is the Copy-number state dropdown (Allelic State, B.23), which is a category not a number. Used by the ctDNA Bundle's intragenic-CNV and multi-gene-CNV Observations - not the structural-variant (translocation-style) Observation, where a copy number doesn't apply. 0..1 display Value Set:
..... LRI/B.32 Structural Variant Inner Start-End 0..1 string Definition: Observation.component.valueRange
Value Set:
...... LRI/B.32-designNote LRI row B.32, OBX type NR, R/O/C = O, [0..1], OBX-4 sub-ID "2a.1". FHIR Variant profile slice: `inner-start-end`. Not a discrete iGene field - summarised within iGene's Genomic_coordinates field. Used by the ctDNA Bundle's intragenic-CNV, multi-gene-CNV and structural-variant Observations. 0..1 display Value Set:
.... NoLRIEquivalent FHIR/iGene Elements With No LRI Discrete Variant Panel Row 0..1 group Definition: Observation.component
Value Set:
..... NoLRIEquivalent-designNote These are used by a current FHIR example and/or iGene, but have no row anywhere in LRI's Discrete Variant Panel (Table 5-2/5-3) - see the Description's gap notes. 0..1 display Value Set:
..... FHIR/CoordinateSystem Coordinate System 0..1 choice Definition: Observation.component.valueCodeableConcept
Value Set:
...... FHIR/CoordinateSystem-designNote No LRI row. FHIR Variant profile slice: `coordinate-system`. Not a discrete iGene field - summarised within iGene's Genomic_coordinates field. Used by all four ctDNA Bundle Observations (1-based character counting). 0..1 display Value Set:
..... FHIR/OriginOfGermlineVariant Origin of Germline Genetic Variant 0..1 choice Definition: Observation.component.valueCodeableConcept
Value Set:
...... FHIR/OriginOfGermlineVariant-designNote No dedicated LRI row - the closest LRI concept is Allelic Phase (82120-7, row B.26), whose answer list happens to include Maternal/Paternal among several "set of variants in cis" options, not a dedicated parent-of-origin field. FHIR Variant profile slice: `variant-inheritance`. iGene: this is the Inheritance field for the four variant types that have one (not LOH), though iGene's own spec gives it no LOINC code. Used by the ctDNA Bundle's small-variant, intragenic-CNV and multi-gene-CNV Observations (Maternal) - not the structural-variant Observation. 0..1 display Value Set:
.... LossOfHeterozygosity Loss of Heterozygosity (iGene fields, mapped to a separate Molecular Consequence Observation) 0..1 group Definition: Observation
Value Set:
..... LossOfHeterozygosity-designNote One of iGene's five variant types (`LOH1`-`LOH2`), with no corresponding row anywhere in LRI's Discrete Variant Panel. Decided: this IG models LOH as a separate [Molecular Consequence](StructureDefinition-MolecularConsequence.html) Observation, `derivedFrom` the `Variant` it accompanies, with a `functional-effect` component coded `SO_0001786 loss_of_heterozygosity` - see [Observation-ctdna9737383222-seqv1-loh](Observation-ctdna9737383222-seqv1-loh.html) for a worked example - rather than as items directly on this Discrete Variant Panel. The two items below describe iGene's own flat fields for reference, not how this IG models them. 0..1 display Value Set:
..... iGene/LOH_Description Gene(s) 0..1 string Definition: Observation.component.valueCodeableConcept
Value Set:
..... iGene/LOH_State Loss of Heterozygosity (LOH) 0..1 choice Definition: Observation.component.valueCodeableConcept
Value Set:
...... iGene/LOH_State-designNote No LOINC code in iGene's own spec ("None"); iGene example value "Significant LOH". Not a value LRI's Allelic State (B.23) answer list supports. 0..1 display Value Set:

doco Documentation for this format

Profile: Questionnaire

Discrete Variant Panel

  • linkId: DiscreteVariantPanel
  • Definition:: Observation
  • Answers:

LRI Table 5-2 row B - repeats for each discrete variant reported (OBX-4 sub-ID "2a", incrementing per repeat).

  • linkId: DiscreteVariantPanel-designNote
  • Answers:

Variant Category

LRI row B.1, OBX type CWE, R/O/C = O, [0..1]. LRI's own answer list (LL4165-8) only distinguishes Simple Variant vs Structural Variant - not granular enough to route a variant to the correct iGene slot type. Resolved: this IG binds this component to its own [IGeneVariantCategory](CodeSystem-IGeneVariantCategory.html) value set instead (`SEQV`/`ICNV`/`MCNV`/`SV`/`LOH`), making the classification that used to be inferred (see [OMICS DSS Result Integration](reportable-variants.html#outstanding-issues)) an explicit, coded value - the FHIR Variant profile has no named slice for this at all, so it is modelled here as an open-slice component, same as `Variant.component:variant-category`. Populated by every current example.

  • linkId: LRI/B.1-designNote
  • Answers:

Transcript Specification

Gene Studied

LRI row B.3, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile: this IG's own `gene-studied` addition (not one of the international profile's named slices). iGene: rolled into the free-text Description field (SEQV/ICNV) or the Gene(s) field (LOH). Used by NTHL1, CFTR, EGFR-ctDNA, and the ctDNA Bundle's small-variant and intragenic-CNV Observations.

  • linkId: LRI/B.3-designNote
  • Answers:

Transcript Reference Sequence

LRI row B.4, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice: `representative-transcript-ref-seq`. iGene: rolled into the free-text Description field (SEQV/ICNV). Used by NTHL1, CFTR and the ctDNA Bundle's small-variant Observation.

  • linkId: LRI/B.4-designNote
  • Answers:

DNA Change (c.HGVS)

LRI row B.5, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice: `representative-coding-hgvs`. iGene: rolled into the free-text Description field (SEQV/ICNV). Used by EGFR-ctDNA, BRCA1 and the ctDNA Bundle's small-variant Observation.

  • linkId: LRI/B.5-designNote
  • Answers:

Amino Acid Change (pHGVS)

LRI row B.6, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice: `representative-protein-hgvs`. iGene: rolled into the free-text Description field (SEQV only - ICNV's Description omits this). Used only by the ctDNA Bundle's small-variant Observation.

  • linkId: LRI/B.6-designNote
  • Answers:

DNA Change Type

LRI row B.7, OBX type CWE, R/O/C = O, [0..1]. FHIR Variant profile slice: `coding-change-type`. Not a discrete iGene field - summarised within iGene's free-text Description/Genomic_coordinates fields. Used by every current example (Sequence Ontology or LOINC answer coding, e.g. duplication, deletion, substitution, copy_number_variation).

  • linkId: LRI/B.7-designNote
  • Answers:

Genomic Specification

Genomic Reference Sequence

LRI row B.9, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice: `genomic-ref-seq`. iGene: rolled into the free-text Genomic_coordinates field (all four variant types). Used by NTHL1 and all four ctDNA Bundle Observations.

  • linkId: LRI/B.9-designNote
  • Answers:

Genomic DNA Change (gHGVS)

LRI row B.10, OBX type CWE, R/O/C = C, [0..1]. FHIR Variant profile slice: `genomic-hgvs`. iGene: rolled into the free-text Genomic_coordinates field (all four variant types). Used by all four ctDNA Bundle Observations - not by NTHL1/CFTR, where it is commented out pending a confirmed mapping.

  • linkId: LRI/B.10-designNote
  • Answers:

Genomic Ref Allele

LRI row B.11, OBX type ST, R/O/C = C, [0..1]. FHIR Variant profile slice: `ref-allele`. Not a discrete iGene field - summarised within iGene's Genomic_coordinates field. Used by NTHL1, CFTR and all four ctDNA Bundle Observations.

  • linkId: LRI/B.11-designNote
  • Answers:

Genomic Allele Start-End

LRI row B.12, OBX type NR, R/O/C = C, [0..1]. FHIR Variant profile slice: `exact-start-end`. Not a discrete iGene field. Used only by the ctDNA Bundle's small-variant Observation - a Range with only the low bound populated.

  • linkId: LRI/B.12-designNote
  • Answers:

Genomic Alt Allele

LRI row B.13, OBX type ST, R/O/C = C, [0..1]. FHIR Variant profile slice: `alt-allele`. Not a discrete iGene field - summarised within iGene's Genomic_coordinates field. Used by the ctDNA Bundle's intragenic-CNV, multi-gene-CNV and structural-variant Observations (as symbolic ALT alleles, e.g. "<DEL>") - not by the small-variant Observation, NTHL1 or CFTR.

  • linkId: LRI/B.13-designNote
  • Answers:

Other Attributes

Cytogenetic (Chromosome) Location

LRI row B.17, OBX type CWE, R/O/C = O, [0..1]. Not one of the international FHIR Variant profile's named component slices (its closest named slice, Cytogenomic Nomenclature 81291-7, is actually a different LRI field - Table 5-1 row A.11, part of the report-level Master Panel, not this Discrete Variant Panel) - captured here as an open-slice addition, consistent with GenomicObservation's open component slicing. iGene: this is the sole field for the Multigenic CNV Description, and part of the Genomic_coordinates field for the other three variant types. Used only by the ctDNA Bundle's multi-gene-CNV Observation (e.g. "Xq22.1-q28").

  • linkId: LRI/B.17-designNote
  • Answers:

Genomic Source Class

LRI row B.18, OBX type CNE, R/O/C = R (required when present), [0..*]. FHIR Variant profile slice: `genomic-source-class`. Not a discrete iGene field. Used by NTHL1, CFTR, EGFR-ctDNA and the ctDNA Bundle's small-variant, intragenic-CNV and multi-gene-CNV Observations (Germline or Somatic) - not by the structural-variant Observation.

  • linkId: LRI/B.18-designNote
  • Answers:

Interpretations

Classification

LRI row B.20 (LRI names it "Genetic sequence variation clinical significance"), OBX type CNE, R/O/C = O, [0..1]. FHIR Variant profile: not one of the profile's own component slices (the profile relies on the generic `Observation.interpretation`/`valueCodeableConcept` pattern for this) - modelled here as an open-slice component to match how every current example actually carries it. iGene: this is the Classification field for all four variant types. Used by all four ctDNA Bundle Observations (e.g. "Pathogenic").

  • linkId: LRI/B.20-designNote
  • Answers:

Allelic State/Phase Information

Allelic State

LRI row B.23, OBX type CNE, R/O/C = C, [0..1], answer list LL381-5 (Heteroplasmic/Homoplasmic/Homozygous/Heterozygous/Hemizygous - no "Loss of Heterozygosity" option). FHIR Variant profile slice: `allelic-state`. iGene: the Zygosity/Copy-number state field for all five variant types (iGene's LOH "State" field has no LOINC code and is a different concept - LRI has no LOH answer here). Used by NTHL1, CFTR, BRCA1 and the ctDNA Bundle's small-variant Observation (Heterozygous).

  • linkId: LRI/B.23-designNote
  • Answers:

Allelic Frequency

LRI row B.24 (LRI names it "Allelic Frequency [NFr]", the FHIR profile and our examples call it "Sample variant allelic frequency [NFr]" - same LOINC code, slightly different display text), OBX type NM, R/O/C = C, [0..1]. FHIR Variant profile slice: `sample-allelic-frequency`. iGene: the Level (VAF %) field for the four variant types that have one (not LOH). Used by EGFR-ctDNA (as a percentage) and all four ctDNA Bundle Observations (as a decimal fraction) - the units differ between the two sources.

  • linkId: LRI/B.24-designNote
  • Answers:

Structural Variant Addenda

LRI Table 5-3 - part of the same Discrete Variant Panel in the HL7 v2 message, shown as a separate table in LRI purely for visual separation of structural-variant-only attributes.

  • linkId: StructuralVariantAddenda-designNote
  • Answers:

Genomic Structural Variant Copy Number

LRI row B.28, OBX type NM, R/O/C = O, [0..1], OBX-4 sub-ID "2a.1". FHIR Variant profile slice: `copy-number`. Not a discrete iGene field - the closest iGene concept is the Copy-number state dropdown (Allelic State, B.23), which is a category not a number. Used by the ctDNA Bundle's intragenic-CNV and multi-gene-CNV Observations - not the structural-variant (translocation-style) Observation, where a copy number doesn't apply.

  • linkId: LRI/B.28-designNote
  • Answers:

Structural Variant Inner Start-End

LRI row B.32, OBX type NR, R/O/C = O, [0..1], OBX-4 sub-ID "2a.1". FHIR Variant profile slice: `inner-start-end`. Not a discrete iGene field - summarised within iGene's Genomic_coordinates field. Used by the ctDNA Bundle's intragenic-CNV, multi-gene-CNV and structural-variant Observations.

  • linkId: LRI/B.32-designNote
  • Answers:

FHIR/iGene Elements With No LRI Discrete Variant Panel Row

These are used by a current FHIR example and/or iGene, but have no row anywhere in LRI's Discrete Variant Panel (Table 5-2/5-3) - see the Description's gap notes.

  • linkId: NoLRIEquivalent-designNote
  • Answers:

Coordinate System

No LRI row. FHIR Variant profile slice: `coordinate-system`. Not a discrete iGene field - summarised within iGene's Genomic_coordinates field. Used by all four ctDNA Bundle Observations (1-based character counting).

  • linkId: FHIR/CoordinateSystem-designNote
  • Answers:

Origin of Germline Genetic Variant

No dedicated LRI row - the closest LRI concept is Allelic Phase (82120-7, row B.26), whose answer list happens to include Maternal/Paternal among several "set of variants in cis" options, not a dedicated parent-of-origin field. FHIR Variant profile slice: `variant-inheritance`. iGene: this is the Inheritance field for the four variant types that have one (not LOH), though iGene's own spec gives it no LOINC code. Used by the ctDNA Bundle's small-variant, intragenic-CNV and multi-gene-CNV Observations (Maternal) - not the structural-variant Observation.

  • linkId: FHIR/OriginOfGermlineVariant-designNote
  • Answers:

Loss of Heterozygosity (iGene fields, mapped to a separate Molecular Consequence Observation)

  • linkId: LossOfHeterozygosity
  • Definition:: Observation
  • Answers:

One of iGene's five variant types (`LOH1`-`LOH2`), with no corresponding row anywhere in LRI's Discrete Variant Panel. Decided: this IG models LOH as a separate [Molecular Consequence](StructureDefinition-MolecularConsequence.html) Observation, `derivedFrom` the `Variant` it accompanies, with a `functional-effect` component coded `SO_0001786 loss_of_heterozygosity` - see [Observation-ctdna9737383222-seqv1-loh](Observation-ctdna9737383222-seqv1-loh.html) for a worked example - rather than as items directly on this Discrete Variant Panel. The two items below describe iGene's own flat fields for reference, not how this IG models them.

  • linkId: LossOfHeterozygosity-designNote
  • Answers:

Gene(s)

Loss of Heterozygosity (LOH)

No LOINC code in iGene's own spec ("None"); iGene example value "Significant LOH". Not a value LRI's Allelic State (B.23) answer list supports.

  • linkId: iGene/LOH_State-designNote
  • Answers:

Profile: Questionnaire

LinkIDDescription & Constraintsdoco
.. DiscreteVariantPanel Definition: Observation
Value Set:
... DiscreteVariantPanel-designNote Value Set:
... LRI/B.1 Definition: Observation.component.valueCodeableConcept
Value Set:
.... LRI/B.1-designNote Value Set:
... TranscriptSpecification Definition: Observation.component
Value Set:
.... LRI/B.3 Definition: Observation.component.valueCodeableConcept
Value Set:
..... LRI/B.3-designNote Value Set:
.... LRI/B.4 Definition: Observation.component.valueCodeableConcept
Value Set:
..... LRI/B.4-designNote Value Set:
.... LRI/B.5 Definition: Observation.component.valueCodeableConcept
Value Set:
..... LRI/B.5-designNote Value Set:
.... LRI/B.6 Definition: Observation.component.valueCodeableConcept
Value Set:
..... LRI/B.6-designNote Value Set:
.... LRI/B.7 Definition: Observation.component.valueCodeableConcept
Value Set:
..... LRI/B.7-designNote Value Set:
... GenomicSpecification Definition: Observation.component
Value Set:
.... LRI/B.9 Definition: Observation.component.valueCodeableConcept
Value Set:
..... LRI/B.9-designNote Value Set:
.... LRI/B.10 Definition: Observation.component.valueCodeableConcept
Value Set:
..... LRI/B.10-designNote Value Set:
.... LRI/B.11 Definition: Observation.component.valueString
Value Set:
..... LRI/B.11-designNote Value Set:
.... LRI/B.12 Definition: Observation.component.valueRange
Value Set:
..... LRI/B.12-designNote Value Set:
.... LRI/B.13 Definition: Observation.component.valueString
Value Set:
..... LRI/B.13-designNote Value Set:
... OtherAttributes Definition: Observation.component
Value Set:
.... LRI/B.17 Definition: Observation.component.valueCodeableConcept
Value Set:
..... LRI/B.17-designNote Value Set:
.... LRI/B.18 Definition: Observation.component.valueCodeableConcept
Value Set:
..... LRI/B.18-designNote Value Set:
... Interpretations Definition: Observation.component
Value Set:
.... LRI/B.20 Definition: Observation.component.valueCodeableConcept
Value Set:
..... LRI/B.20-designNote Value Set:
... AllelicStatePhase Definition: Observation.component
Value Set:
.... LRI/B.23 Definition: Observation.component.valueCodeableConcept
Value Set:
..... LRI/B.23-designNote Value Set:
.... LRI/B.24 Definition: Observation.component.valueQuantity
Value Set:
..... LRI/B.24-designNote Value Set:
... StructuralVariantAddenda Definition: Observation.component
Value Set:
.... StructuralVariantAddenda-designNote Value Set:
.... LRI/B.28 Definition: Observation.component.valueQuantity
Value Set:
..... LRI/B.28-designNote Value Set:
.... LRI/B.32 Definition: Observation.component.valueRange
Value Set:
..... LRI/B.32-designNote Value Set:
... NoLRIEquivalent Definition: Observation.component
Value Set:
.... NoLRIEquivalent-designNote Value Set:
.... FHIR/CoordinateSystem Definition: Observation.component.valueCodeableConcept
Value Set:
..... FHIR/CoordinateSystem-designNote Value Set:
.... FHIR/OriginOfGermlineVariant Definition: Observation.component.valueCodeableConcept
Value Set:
..... FHIR/OriginOfGermlineVariant-designNote Value Set:
... LossOfHeterozygosity Definition: Observation
Value Set:
.... LossOfHeterozygosity-designNote Value Set:
.... iGene/LOH_Description Definition: Observation.component.valueCodeableConcept
Value Set:
.... iGene/LOH_State Definition: Observation.component.valueCodeableConcept
Value Set:
..... iGene/LOH_State-designNote Value Set:

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