It is the soil pipe, which provides an air vent for the foul drainage. The flashing around it has failed, probably because it isn't a proper lead tile, but some cheap aluminium or plastic arrangement. As Slimjim says you could remove it and fit an air admittance valve if you are sure there is no chance of a gas buildup because the system is vented to air elsewhere. Worth mentioning that the air admittance valves come in packaging with a polystyrene cup over the top of the vent. This is NOT packaging -it is insulation to stop moisture freezing and the valve jamming shut. I have seen dozens of installations where this insulation has been mistakingly taken off.
You will have to have the roof repaired and the tile/flashing replaced Shygirl. You won't achieve anything from inside with silicone. I would have a proper lead tile fitted with a solvent welded seal between the pipe and the lead, which may mean renewing the top section of pipe as well. (I am a qualified plumber). Sorry, but this necessary work won't be cheap.