“I'm sorry, but can you clarify what it is you're asking about?”
You got an email from a coworker asking a question. You read the email and you understood the meaning of the words and sentences, but you can't understand the overall question because the writing wasn't very clear. You write this in response.
I'm sorry, but can you clarify what it is you're asking about?
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Use this in writing to introduce a question that's inconvenient for the reader. In spoken English, the phrase "I'm sorry, but..." can sound a little angry depending on how you say it. Instead, I usually just say something like:
I'm sorry. What was it you're asking about?
To "clarify" something that you said means to make it clear. When you've said something that might be confusing or was misunderstood, you "clarify" your statement by saying it again in a new way and adding more details. The word "clarify" can be used in questions like in the example above, or in the phrase "To clarify,..."
Just to clarify, you said that you're definitely coming, right?
You often hear the noun form of "clarify", which is "clarification":
I wrote back to her and asked for clarification, but she never returned my e-mail.
A simpler version of the question above is:
Can you clarify what you're asking about?
But using "what it is" instead of just "what" places extra emphasis on the question. People often use this expression to show a deeper level of confusion.