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For example, the CNERY transition,* how exactly is this pronounced? On the VATSIM community, it seems there's a huge debate on what this is called. Some people say CONNERY, and some people say SCENERY. I personally say SCENERY since it makes more sense, but what is the most proper one? And is there a place where we can find pronunciation of such things?

Like another one is SCTRR transition which some people say SCOOTER, some people say SCATTER.

* CNERY transition is part of KLAX's DOTSS TWO DEPARTURE.

It would be nice if there were an authoritative, canonical, source for these sorts of waypoints, but sadly, I don't think one exists. I say that because I hear controllers sometimes using a different set of vowels or syllable emphasis "today" than they did "yesterday". If there were a single "right" way to verbalize CNERY or SCTRR, I'd expect ATC to have them all down. But in plenty of cases beyond those two, it remains unclear.

For example, the JFRYE arrival into Dallas -- is it the "Jeffrey" or the "J-Fry" arrival? You hear both from Ft Worth Center all the time.

My conclusion: no cannonical source exists.

If a word was used to choose a pronounceable 5-letter designator (name-code), it would not be documented. (There are many pronounceable name-codes that don't mean a thing – in both English and the local language.)

ICAO Annex 11 (Air Traffic Services) Appendix 2 says:

4.2 In printed and coded communications, only the coded designator or the selected name-code shall be used to refer to a significant point.

So don't expect to find any mention other than the 5-letter code, which has to be pronounceable for some fixes:

For the USA, Order 8260.19H says:

Pronounceable fix names. Except as stated in paragraph 2-10-5.a(3), all fix names serving any IFP must be pronounceable.

Which Annex 11 points out as:

Where a significant point is required at a position not marked by the site of a radio navigation aid, the significant point shall be designated by a unique five-letter pronounceable "name-code". This name-code designator then serves as the name as well as the coded designator of the significant point.

XKCDQ would not be a pronounceable name, but CNERY would. If you did not comprehend whatever name the controller used, say you're flying in a new area with little traffic around you (prior comms to/from other traffic help you in anticipating things like that), you can simply ask the controller, "Say again in phonetic alphabet."

Sometimes the airspace designers come up with funny sequences though, e.g., see: Anybody know the reason for the ‘Star Wars’ themed STARs into KATL?

(All emphasis mine.)

There is no single "correct" pronunciation for fix/waypoint names. The only rule is that the pronunciations must be unambiguous with respect to all other nearby names. For CNERY, jf one controller says "Scenery" and another says "Connery", and neither is ambiguous, then both are arguably correct. Heck, I'd even accept "Canary"; maybe the local fixes are named after birds but CNARY was already in use elsewhere.

As a practical matter, pilots should read things back the same way the controller said them. The point of communication is to be understood, so as long as that's happening, the details aren't important.