Emedgene uses VEP and EFF for transcript annotations and in upcoming versions will be adding Illumina Connected Annotations.
Each variant has a "main_effect" and "main_gene" chosen based on the most prioritized transcript for this variant. Transcript prioritization depends on many different parameters and on different Emedgene pipeline versions.
Here is a list of ordered rules for transcript prioritization:
VEP transcripts are prioritized over EFF transcripts.
If the case is a virtual panel, prioritize transcripts from genes in the case gene list (but not for Boosted Genes type panels).
Prioritize RNA genes associated with disease (See appendix 1 for prioritized list RNA genes). Importantly this does not apply to upstream and downstream RNA variants.
De-prioritize biotype readthrough transcripts.
Prioritize based on impact in the following order: HIGH > MODERATE > LOW > MODIFIER.
Prioritize introns over UTR over upstream (Appendix 2: MODIFIER effects prioritization).
Prioritize organization canonical transcripts (Defined in Curate).
Prioritize canonical transcripts (Based on Appris).