How can I repair a bump in a wooden desk?
You will not make the crack go away, at least not with out destroying the texture of the finish. If the core material is particle board, it will be even more difficult. You could, as mentioned in the comment put something over it to flatten it, but it will take a driving force to set it back flush, or near flush. 

This is where particle board will NOT treat you right. Since it is made up of fine wood particles, when the screw goes through, it displaces the particles and they will never go back exactly as they were. A small block of wood with a hammer driving on it MAY flatten it out some, by recompressing the particles of sawdust. It may also make the chips come out the rest of the way.

If it does work, you may want to try some appliance repair paint to fill in the crack after it has been flattened a bit or perhaps leave it just as it is. Use the appliance paint on the crack, work it in and remove the excess on the surface, leaving the paint in the crack. Hopefully it will disguise the crack to a degree. 

Test the paint on a hidden surface with the same finish you need to repair, in case the appliance paint is lacquer based too. If it is, it will "melt" the existing finish and change the texture in the immediate area of the crack. Hopefully it will wipe off clean with no change in the surface at all.