Genotype prediction from RNA-seq data has become widespread. RNA-seq data, unlike DNA-seq data, are available as raw reads for many projects, with related protocols and consent terms typically inaccessible. However, there is a lack of clarity in current policy and inconsistency in practice with regard to the handling of these data. Here, we call for a framework for management of RNA-seq data and the predicted genotypes that includes registered access for RNA-seq data, controlled access for predicted genotypes, and a code of conduct for data access and use, as well as enhanced downstream protections.