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Yes, you do need to file Form 5329.
You can file the Form 5329, to calculate any penalty and/or request a waiver, using the steps below. It would self generate when you answer the questions about your Form 1099-R. If possibly in your case you do not have a Form 1099-R or the one you have is RMD so the prompt is not forthcoming. Because you did not take the required minimum distribution (RMD) then you must add the form to your return.
You must include form 5329 when you e-file and unfortunately this can only be done using the 'Forms' mode which is only available with TurboTax Desktop if you do not have a 1099-R to file.
Once this is completed here are the steps to add Form 5329 to your return.
You will not pay any penalty now until the IRS determines if it will grant the waver, then they will inform you if you owe the penalty.
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