In this large-scale two-sample MR study of alternative splicing assessed for their effect upon three COVID-19 outcomes in up to 122,616 COVID-19 cases and 2,475,240 population controls, we provide evidence that alternative splicing of OAS1, ATP11A, DPP9 and NPNT in lung influences COVID-19 severity, and alternative splicing of MUC1 and PMF1 in lung influences COVID-19 susceptibility. Here, DPP9 is linked to COVID-19.