Depending on location, there are primarily two different types of plumbing vent flashing. The most common in northern climates is the neoprene or metal boot. In Florida and in many other southern states, a lead flashing, which also protects the plastic vent pipe from ultraviolet damage, is more common.
The stack vent is provided for the waste stack. The stack vent is the extension of a soil or waste stack above the highest horizontal drain that is connected to the stack. This is the main commonly-observed pipe that is observed penetrating the sloped roof surface, and it may also be visible in the unfinished attic space.
This is an inspection image of a stack vent pipe penetrating the roof covering surface.
Most skylights show signs of moisture penetration. This is especially a problem when the roof has been re-covered and the original flashing were damaged while being removed and re-installed. Credit to InterNachi. www.swordroof.com