include variant and phenotype score in the JSON output

[MattWellie]

Purpose

• The whole-cohort JSON aggregation of the Variant TSVs doesn't currently collect the phenotype/variant scores required to run cross-exomiser-version deltas using the suggested parameters from https://pmc.ncbi.nlm.nih.gov/articles/PMC11655964/

Proposed Changes

• adds Pheno, Gene_variant, and Variant scores into the JSON summary file