Welcome to the community, Mette!
If only you had posted this yesterday, you could have joined us at the -omics subgroup meeting earlier today 
. At the Oncology WG, we have a dedicated subgroup focused on bringing -omics data into OMOP. We have developed conventions and standard vocabularies (i.e, OMOP Genomics) to represent variation at the gene, transcript, and protein levels. Most of the work so far has focused on somatic variation, but the underlying principles are the same, and there are ongoing discussions with folks interested in non cancer use cases on how to align and organize things without reinventing the wheel again. We are also in the early stages of kicking off an update to the OMOP Genomics vocabulary, so this is very timely.
Please join us. We would love to hear your wish list and plan together. We meet on the 2nd and 4th Tuesdays of the month from 9 to 10 am EST.