Pathogenicity qualifiers

[ahwagner]

@larrybabb I think we want to use a MappableConcept for the penetrance qualifier below, right?

va-spec/schema/va-spec/base/va-core-source.yaml

Lines 980 to 989 in 0228579

	penetranceQualifier:
	type: string
	enum:
	- high
	- low
	- risk allele
	description: >-
	Reports the penetrance of the pathogenic effect - i.e. the extent to which the
	variant impact is expressed by individuals carrying it as a measure of the
	proportion of carriers exhibiting the condition.

And do we want to support multiple modes of inheritance in the mode of inheritance qualifier below? If so, should we be clearer about the semantics of what multiple modes mean? Do we want to leave this as Coding, or use MappableConcept here as well?

va-spec/schema/va-spec/base/va-core-source.yaml

Lines 990 to 997 in 0228579

	modeOfInheritanceQualifier:
	type: array
	ordered: false
	items:
	$ref: "/ga4gh/schema/gks-core/1.x/json/Coding"
	description: >-
	Reports a pattern of inheritance expected for the pathogenic effect of the variant.
	Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify.

[ahwagner]

we will also add shared alleleOriginQualifier with MappableConcept

[larrybabb]

lgtm