@SMK11 well that is a good question. So for transparency,
Form 5329 is filed with your 2022 Form 1040, 1040-SR, or 1040-NR by the due date, including extensions, of your tax return. If you don't have to file a 2022 income tax return, complete and file Form 5329 by itself at the time and place you would be required to file Form 1040, 1040-SR, or 1040-NR.
So since you are filing taxes it should have been filed with the tax return itself rather then with the extension. I cannot find any specific guidance on this specific issue that you are facing. Ultimately, despite the fact that it has been filed by mail, I would make sure it is included with your 2022 filing that you will be completing.
Now the important part you need to reflect the payment made to the IRS. First, check the account that you made the payment from and make sure there is a debit. You may also want to check your IRS account as well if you have one. Then in Turbo Tax Online under Deductions and Credits go to Estimates and Other Taxes Paid. Then Income Taxes Paid and then Payment with Federal Extension.
As long as you properly reflect the payment the inclusion of the Form 5329 should not make a difference as it is a net zero.
All the best,
Marc T.
TurboTax Live Select Time Tax Expert
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