Is it? I can only think of (the very frequently noted) ‘algebra’ and ‘algorithm’.
- azimuth
- zenith
- nadir
Also some chemistry terms, again just from top of brain, might be wrong: - alchemy
- elixir
- arsenic
- alkaliThe difference between an apex and a zenith is that an apex exists as a point in space, while a zenith is a direction, with no fixed point which may be said to be "the" zenith. There are other differences given that apex has a few related meanings, but this is the main one.
Edit: I think almost every word with "ph" in it is from Greek and "th" in languages other than English.