Scope and Usage
Variant interpretation criteria are provided as part of frameworks such as the ACMG Guidelines for charaterizing the pathogenicty of genetic variants. These criteria define relevant data types and rules for interpreting this data as evidence, to make a specific type of assertion about a variant that is ultimately relevant to its pathogenicity interpretation. For example, the PM2 ACMG criterion may be met based on a study showing a variant to be absent in a particular population of healthy individuals (e.g. non-Finnish Europeans in the ExAC database). Implicit in an this criterion being 'met' is the broader assertion that the frequency of the variant is sufficiently low in healthy populations to support a meaningful argument for the pathogenicity of the variant.
In the process of generating a variant interpretation through the ACMG workflow, criterion assessments are treate as 'intermediate' assertions that establish whether a particuar criterion is met or not for the variant under review. Evidence relevant to the merit of this assertion is organized around one or more evidence lines, and the criterion assessment is itself used as evidence for the final interpretation of the variant's pathogenicity.
Attributes
Name | Type | Cardinality | Description | IRI | Defined in |
---|---|---|---|---|---|
criterion | Criterion | 0..1 | The rule describing how the data is being used | SEPIO:0000041 | CriterionAssessment |
variant | CanonicalAllele | 1..1 | Variant about which the assemssment is made | SEPIO:0000275 | CriterionAssessment |
statementOutcome | @id | 1..1 | Result of assessing the data and criterion | SEPIO:0000197 | CriterionAssessment |
condition | GeneticCondition | 0..* | Condition for which the assessment is made | SEPIO:0000276 | CriterionAssessment |
label | string | 0..1 | A name given to the resource. | RDFS:label | Entity |
description | string | 0..1 | Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource. | DC:description | Entity |
userLabelDictionary | UserLabel | 0..* | An optional label defined by the user. Used for custom entities or to clarify the preferred user label on existing entities with non-preferred labels. | SEPIO:0000422 | Statement |
outcomeQualifier | string | 0..1 | Use “NOT” as the value of this property to assert that the statement is negated. | SEPIO:0000346 | Statement |
evidenceLine | EvidenceLine | 0..* | supporting evidence | SEPIO:0000006 | Statement |
contribution | Contribution | 0..* | The contributions (agent, time and role) made to this entity | SEPIO:0000159 | Statement |
source | string | 0..* | A string indicating the source of a Statement | DC:source | Statement |