Its time rethink on your meta model. Try to keep your meta model as flexible so as to support all such sort of operation. In other words your meta model's compound key combination should have the flexibility to handle such deletion or updation related queries.
Now coming to your example if you want update the freq column, then first of all you have to remove the row with that freq value, then re-insert a proper combination. Try to remove the row using your compound key combination, say in your case,
delete from users where id ='key' AND freq= 3
And then you can insert a fresh new row.