This is a revision from my earlier post. I agree with DanaB27 that $5500 should be entered in Box 1 of the 1099R and 0 in Box 2A.
You will still enter $6,000 on the penalty screen as withdrawn by the due date during the IRA contribution interview (Federal > Deductions and Credits > Traditional and Roth IRA Contributions. "Contribution withdrawn before due date of your return").
{Edited 04/05/23} (1:236 PM PST} @jac310
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