Water heater vent pipe scorching roof

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It should be a B vent, double wall, going thru an attic space. 6ā€ clearance around combustible on a C vent, single wall. That to me, doesnā€™t look like charring. You could paint that area and keep an eye on it to see if it discolors again. Was this here maybe before you got the place? Maybe previously the vent didnā€™t extend all the way up to the roof Jack and was resolved but the discoloration was never bothered with?
 
Putting a new rubber boot over this pipe requires you to lift some shingles.
I'm with old dog... no rubber against a single wall exhaust pipe...
When I had an old style gas water heater, the flue pipe went into the masonry chimney, not directly through the roof...
 
You might still need to redo some shingles, especially if the new double wall roof stack and flashing is bigger than the existing stack (plumbing drain vent pipe?).
 
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