GenomicInterpretation

This element is used as a component of the Interpretation element, and describes the interpretation for an individual variant or gene. Note that multiple variants or genes may support the interpretation related to one disease. See the Interpretation element for examples.

Data model

GenomicInterpretation

Definition of the GenomicInterpretation element
Field Type Multiplicity Description
subject_or_biosample_id string 1..1 The id of the patient or biosample that is the subject being interpreted. REQUIRED.
interpretation_status enum InterpretationStatus 1..1 status of the interpretation. REQUIRED.
call oneof {GeneDescriptor | VariantInterpretation} 1..1 represents the interpretation. REQUIRED.

InterpretationStatus

Definition of the InterpretationStatus enumeration
Name Ordinal Description
UNKNOWN_STATUS 0 No information is available about the status
REJECTED 1 The variant or gene reported here is interpreted not to be related to the diagnosis
CANDIDATE 2 The variant or gene reported here is interpreted to possibly be related to the diagnosis
CONTRIBUTORY 3 The variant or gene reported here is interpreted to be related to the diagnosis
CAUSATIVE 4 The variant or gene reported here is interpreted to be causative of the diagnosis

Example

genomicInterpretation:
    subjectOrBiosampleId: "subject 1"
    interpretationStatus: "CONTRIBUTORY"
    variantInterpretation:
      acmgPathogenicityClassification: "PATHOGENIC"
      variationDescriptor:
        expressions:
        - syntax: "hgvs"
          value: "NM_001848.2:c.877G>A"
        allelicState:
          id: "GENO:0000135"
          label: "heterozygous"

Explanations

subject_or_biosample_id

Each genomic interpretation is based on a genomic finding in the germline DNA of the Individual referenced in the phenopacket or of a Biosample derived from the individual. The id used here must therefore match with the Individual.id or with the Biosample.id element.

interpretation_status

This is an enumeration that describes the conclusion made about the genomic interpretation.

  • UNKNOWN_STATUS: unknown
  • REJECTED: the variant or gene reported here is interpreted not to be related to the diagnosis
  • CANDIDATE: the variant or gene reported here is interpreted to possibly be related to the diagnosis
  • CONTRIBUTORY: the variant or gene reported here is interpreted to be related to the diagnosis
  • CAUSATIVE: the variant or gene reported here is interpreted to be causative of the diagnosis

In an autosomal dominant Mendelian disease, one variant is causative. In this case, one would classify it as CAUSATIVE and the Interpretation object that contains the genomic interpretation would use SOLVED. Similarly in the case of an autosomal recessive disease, one would classify a homozygous variant as CAUSATIVE. There are several situations in which one should use CONTRIBUTORY. In the case of an autosomal recessive disease, two CONTRIBUTORY genomic interpretations would be used for compound heterozygous variants. In cancer, CONTRIBUTORY can be used for multiple variants, and the corresponding Interpretation object could classify them as ACTIONABLE, for instance, if a targeted treatment is available for the variant.

call

Either an GeneDescriptor or a VariantInterpretation representing the subject of the genomic interpretation.