MII IG Kerndatensatz-Modul Molekulargenetischer Befundbericht
2027.0.0-ballot.1 -
Germany
MII IG Kerndatensatz-Modul Molekulargenetischer Befundbericht
2027.0.0-ballot.1 -
Germany
This page is part of the MII IG Kerndatensatz-Modul Molekulargenetischer Befundbericht (v2027.0.0-ballot.1: Release) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version. For a full list of available versions, see the Directory of published versions
This page describes the ValueSets of the Molekulargenetischer Befundbericht module (naming
convention MII_VS_<Module>_<Name>). For general guidance on using codes, see
FHIR Terminology; the code systems
the sets draw from are described in the terminology section of this page — the
module does not define a code system of its own.
Expansions: ValueSet expansions in this guide are produced by a FHIR
terminology server — SU-TermServ if the client certificate is configured,
otherwise the public HL7 server tx.fhir.org (in which case some KDS-specific
ValueSets may not expand completely).
The terminology components define the standardized vocabularies for the semantic interoperability of genetic data. The terminologies are organized by their origin:
| Section | Content |
|---|---|
| MII ValueSets | This module's own ValueSets (relationship, family history) |
| Clinical Genomics | ValueSets and CodeSystems from the HL7 Genomics Reporting IG |
| External terminologies | International standards (LOINC, SNOMED CT, HGNC, etc.) with licensing information |
| Source | Use | Example |
|---|---|---|
| MII-defined | Own requirements, no suitable external terminology | Verwandtschaftsgrad, Familiäre Linie |
| Clinical Genomics | Genetics-specific concepts from the STU3 standard | DNA Change Type, Functional Effect |
| External terminology | Established international standards | LOINC, SNOMED CT, HGNC |
| Strength | Meaning | Example |
|---|---|---|
| Required | Exact match required | HGVS notation |
| Extensible | ValueSet may be extended where needed | Diagnosis codes |
| Preferred | Recommended but not mandatory | - |
| Example | Illustrative only, no constraint | - |
This module defines the following ValueSets of its own for the interoperability of molecular genetic reports.
SNOMED CT codes for family members in the context of the family history.
mii-vs-molgen-family-member-snomed
Coding of the degree of relationship for the family history.
mii-vs-molgen-verwandtschaftsgrad
Coding of the type of relationship (biological, legal, etc.).
mii-vs-molgen-verwandtschaftsverhaeltnis
Coding of the family line (maternal, paternal, etc.).
mii-vs-molgen-familiaere-linie
The following ValueSets and CodeSystems are taken from the HL7 Clinical Genomics Reporting Implementation Guide STU3. They are not defined by this module.
The Clinical Genomics IG defines the following CodeSystems, which are used in this module:
| CodeSystem | Description | Canonical URL |
|---|---|---|
| TBD Codes | Temporary codes for Genomics Reporting | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs |
| Molecular Biomarker Ontology | Biomarker categories | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/molecular-biomarker-ontology-cs |
Standardized gene symbols and names from the HUGO Gene Nomenclature Committee. HGNC gene IDs are used with the prefix "HGNC:" as the code and the gene symbol as the display.
Canonical: http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs
Human Genome Variation Society notation for the standardized description of sequence variants.
Canonical: http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs
Types of DNA changes, based on the Sequence Ontology.
Canonical: http://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type-vs
Molecular consequences of a variant at the transcript and protein level.
Canonical: http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-consequence-vs
Functional effects of a variant on biological products or pathways (e.g. loss of function, gain of function).
Canonical: http://hl7.org/fhir/uv/genomics-reporting/ValueSet/functional-effect-vs
Confidence levels for the assessment of a variant.
Canonical: http://hl7.org/fhir/uv/genomics-reporting/ValueSet/variant-confidence-status-vs
Modes of inheritance for genetic diseases (autosomal dominant, recessive, X-linked, etc.).
Canonical: http://hl7.org/fhir/uv/genomics-reporting/ValueSet/condition-inheritance-vs
Example evidence-level codes for the classification of variants.
Canonical: http://hl7.org/fhir/uv/genomics-reporting/ValueSet/evidence-level-example-vs
Therapeutic implications of genetic variants.
Canonical: http://hl7.org/fhir/uv/genomics-reporting/ValueSet/genetic-therapeutic-implications-vs
genetic-therapeutic-implications-vs
Codes for relative interpretations (high, low, normal).
Canonical: http://hl7.org/fhir/ValueSet/observation-interpretation
This module uses international terminology standards for the semantic coding of genetic findings.
| Terminology | Description | URL | License |
|---|---|---|---|
| HGNC | HUGO Gene Nomenclature Committee - standardized gene symbols | http://www.genenames.org/geneId |
CC0 |
| HGVS | Human Genome Variation Society - sequence variant notation | http://varnomen.hgvs.org |
Open |
| ISCN | International System for Human Cytogenomic Nomenclature | - | Commercial |
| Sequence Ontology | Ontology for genomic annotations | http://sequenceontology.org |
CC BY-SA |
| Terminology | Description | URL | License |
|---|---|---|---|
| LOINC | Logical Observation Identifiers Names and Codes | http://loinc.org |
LOINC License - free of charge |
| SNOMED CT | Systematized Nomenclature of Medicine | http://snomed.info/sct |
NRC license |
| ICD-10-GM | ICD-10 German Modification | http://fhir.de/CodeSystem/bfarm/icd-10-gm |
BfArM - free of charge |
| Orphanet | Rare diseases | http://www.orpha.net |
CC BY 4.0 |
| OMIM | Online Mendelian Inheritance in Man | http://www.omim.org |
OMIM License |
| HPO | Human Phenotype Ontology | http://human-phenotype-ontology.org |
Custom - free of charge |
| Database | Description | URL | Notes |
|---|---|---|---|
| RefSeq | NCBI Reference Sequences | http://www.ncbi.nlm.nih.gov/refseq |
Preferred: MANE Select transcripts |
| Ensembl | Ensembl Genome Browser | http://www.ensembl.org |
Alternative transcript references |
| dbSNP | Single Nucleotide Polymorphism Database | http://www.ncbi.nlm.nih.gov/snp |
rs numbers for known variants |
| ClinVar | Clinical Variant Database | http://www.ncbi.nlm.nih.gov/clinvar |
Clinical variant assessments |
| COSMIC | Catalogue of Somatic Mutations in Cancer | https://cancer.sanger.ac.uk/cosmic |
Somatic variants |
| Database | Description | URL | Use |
|---|---|---|---|
| PharmGKB | Pharmacogenomics Knowledge Base | https://www.pharmgkb.org |
Evidence levels for pharmacogenetics |
| CPIC | Clinical Pharmacogenetics Implementation Consortium | https://cpicpgx.org |
Dosing recommendations |
For HGVS notations, MANE Select transcripts should be used preferentially:
NM_007294.4)| Terminology | Recommendation |
|---|---|
| ICD-10-GM | State the annual version (e.g. 2024) |
| LOINC | Document the version at implementation time |
| SNOMED CT | International Edition + German extension |
| RefSeq | Always state the transcript version number |
Using some terminologies requires licensing agreements: