ClinicalVariantProposition

Note

This data class is at a trial use maturity level and may change in future releases. Maturity levels are described in the GKS Maturity Model.

Computational Definition

A proposition for use in describing the effect of variants in human subjects.

Information Model

Some ClinicalVariantProposition attributes are inherited from SubjectVariantProposition.

Field	Flags	Type	Limits	Description
id		string	0..1	The ‘logical’ identifier of the Entity in the system of record, e.g. a UUID. This ‘id’ is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
type		string	1..1	The name of the class that is instantiated by a data object representing the Entity.
name		string	0..1	A primary name for the entity.
description		string	0..1	A free-text description of the Entity.
aliases	⋮	string	0..m	Alternative name(s) for the Entity.
extensions	⋮	Extension	0..m	A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
predicate		string	1..1	The relationship declared to hold between the subject and the object of the Proposition.
object		object	1..1	An Entity or concept that is related to the subject of a Proposition via its predicate.
subjectVariant		MolecularVariation | CategoricalVariant | iriReference	1..1	A variant that is the subject of the Proposition.
geneContextQualifier		Mappable Concept | iriReference	0..1	Reports a gene impacted by the variant, which may contribute to the association described in the Proposition.
alleleOriginQualifier		Mappable Concept | iriReference	0..1	Reports whether the Proposition should be interpreted in the context of a heritable “germline” variant, an acquired “somatic” variant in a tumor, or a post-zygotic “mosaic” variant. While these are the most commonly reported allele origins, other more nuanced concepts can be captured (e.g. “maternal” vs “paternal” allele origin). In practice, populating this field may be complicated by the fact that some sources report allele origin based on the type of tissue that was sequenced to identify the variant, and others use it more generally to specify a category of variant for which the proposition holds. The stated intent of this attribute is the latter. However, if an implementer is not sure about which is reported in their data, it may be safer to create an Extension to hold this information, where they can explicitly acknowledge this ambiguity.