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How do I say, for example, the following sentence/question: "To clarify,
breakfast is at 7:00am?"

I know that 明らめる and 明らかにする both have the meaning "to clarify". But I do not
know if there is a more natural set phrase to use.

Also, I actually do not know how I would use the vocabulary to translate my
sentence anyway. As of now, the translation I would do has multiple sentences:
すみませんですが、少し分からなくて、朝ご飯のことを明らかにして頂けませんか。朝ご飯は午前７時ですね？
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phrases
How to say "To clarify, ...?" in Japanese?
The dictionary definitions 「明{あき}らかにする」 and 「明確{めいかく}にする」 would sound way too
serious for stating/asking about breakfast times.

The most natural phrases I could think of right now would be along the lines
of:

Statement: 「念{ねん}のために言{い}うと、朝食{ちょうしょく}は7時{じ}です。」

Question: 「念{ねん}のためにお聞{き}きしますが、朝食は7時です **ね** 。」 Use a rising intonation at the
end.
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EDITED FROM SHOKO'S CORRECTION:

Agreeing with l'électeur; 明らめる and 明らかにする would sound highly unusual in this
context, no matter how formal the situation calls for you to be. I personally
learned 明らめる as "to explain," whereas a clarification as you've presented is a
confirmation of a fact, not an enlightening explanation as the 明 would
suggest. In your example sentence, 朝ご飯のこと also seems a little excessive for
the topic, unless breakfast is a serious or complicated affair.

As FailyFeely commented, 確認する (and also 確かめる, which may remind you of 確かに, or
"certainly/surely") means "to confirm" or "to verify", so try: **確認したいのですが**
(or just 確認ですが) **、朝ご飯は午前７時ですね/か？**

Using rising intonation for 'ね' is the definition of checking for agreement
when you're partially but not entirely certain of something. FailyFeely's
suggestion itself works too.
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As Faily Feely suggested, 「確認したいのですが」sounds the most natural in this sentence.
You can say 「確認ですが」 too (just less formal). You can also add 「念のため」in front of
either of that, but it pretty much means the same.

Also, I was born and raised in Japan but I've never used or heard the
expression 「明らめる」 except in very old books. (I actually had to Google it! haha
Thank you for teaching though)

Nao
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