Is there a database of disease prevalence?
For rare diseases, you can use Orphanet. You can download an xml file with prevalence from orphadata.

There is an OWL version of Orphanet called ORDO, you can browse it on the EBI Ontology Lookup Service. See for example Arrhythmogenic right ventricular cardiomyopathy and point prevalence relationships in the lower right box. There are a variety of programmatic ways to access this, including the OLS web API, SPARQL queries, or downloading the OWL and using an ontology API.