Is the 5V supply in any way user accessible?
Sounds like no. In this case, the standard 3-4mm clearance is okay. You should use a non-conductive enclosure (plastic). If you need to use metal, then you must earth the enclosure.
A couple other things to keep in mind...Where is the 5V rail coming from? Are you using a isolated converter (with a transformer) or is the 5V rail from a simple non-isolated buck converter directly off the mains?
If the design is not isolated, then you still need to be careful about any controls (knobs or buttons) that are user-facing. Plastic case is good, but be careful about potentiometer shafts, switch actuators, etc. If they are metallic, there may be a fault condition that puts the users in a dangerous situation.
If you are using an isolated design with a transformer, and assuming all controls are on the isolated side of the transformer, then you don't have to worry about the above. However, you do need to be concerned with the level of isolation provided by your isolated AC/DC converter. In this case, it's best to just buy an off the shelf PCB module. But, even with a module, you still need to make sure you have adequate spacing between primary and secondary connections. In this case, most safety standards require at least 5-6mm. Most stringent medical standards need 8mm.