When stratifying patients according to clinical features, we observed a particularly high mutation burden of 181 small somatic variants (SNVs/indels; average among 37 iCCA patients was 74), including two missense mutations in MUC1 and frameshift mutations in ELF3 and AURKAIP1, in‐patient CCC‐036 with primary sclerosing cholangitis (Table S1). Here, ELF3 is linked to sclerosing cholangitis.