The Genomics FHIR Variant spec should have a new component to document the Functional Effect for a specific mutation, corresponding to the values in the Sequence Ontology's concept of Functional Effect: http://sequenceontology.org/browser/current_svn/term/SO:0001536

This would be more aligned with Implications, not necessarily a new component on Variant.

Proposed definition: The effect of a variant on downstream biological products or pathways.

ClinVar has 'Functional Consequence' that is similar, but has little standardization in terminology. There is a range of tools that output values.
https://www.ncbi.nlm.nih.gov/variation/docs/glossary/
Functional consequence
Functional consequence is an observed effect of a sequence change on function. Ontologies such as VariO and Sequence Ontology (SO) are used to standardize terms, which are documented here: ftp://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/functional_consequence.txt. As used by NCBI's resources, functional consequence is experimentally determined, in contrast to molecular consequence, which is computed from sequence annotation.

Compare:
molecular consequence: a calculation of the effect of the sequence change, reported per transcript. ClinVar calculates the predicted molecular consequence, but does not predict functional consequence.
Functional consequence (e.g. quantitative effects on gene expression, alternative splicing) is based on experimental evidence and must be submitted.