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You did it wrong in 2015 and need to amend 2015. You cannot report a RMD in 2015 if it was not distributed until 2016. It can only be reported in the tax year distributed - 2016. The 2016 1099-R would have both RMD's on it and must be reported on your 2016 tax return. Yes, you will pay tax on it, and that should be recovered when you amend 2015 to get back any tax erroneously paid in 2015 if you paid the tax in 2015.
What you need to do is amend 2015 and remove the substitute 1099-R (the 4852 form and the associated 1099-R that it created). Then attach a 2015 5329 form requesting a waiver of the missed RMD penalty as follows.
From 5329 instructions:
Waiver of tax.
The IRS can waive part or all of this tax if you can show that any shortfall in the amount of distributions was due to reasonable error and you are taking reasonable steps to remedy the shortfall. If you believe you qualify for this relief, attach a statement of explanation and file Form 5329 as follows.
1. Complete lines 52 and 53 as instructed.
2. Enter “RC” and the amount you want waived in parentheses on the dotted line next to line 54. Subtract this amount from the total shortfall you figured without regard to the waiver, and enter the result on line 54.
3. Complete line 55 as instructed. You must pay any tax due that is reported on line 55.
The IRS will review the information you provide and decide whether to grant your request for a waiver.
(The waiver would only be denied if there is no reasonable explanation and the missed RMD was not taken at all.)
You can download the 2015 5329 form from the IRS.
Enter 5329 in the find box and download the 2015 5329 form and instructions.
https://apps.irs.gov/app/picklist/list/priorFormPublication.html
You did it wrong in 2015 and need to amend 2015. You cannot report a RMD in 2015 if it was not distributed until 2016. It can only be reported in the tax year distributed - 2016. The 2016 1099-R would have both RMD's on it and must be reported on your 2016 tax return. Yes, you will pay tax on it, and that should be recovered when you amend 2015 to get back any tax erroneously paid in 2015 if you paid the tax in 2015.
What you need to do is amend 2015 and remove the substitute 1099-R (the 4852 form and the associated 1099-R that it created). Then attach a 2015 5329 form requesting a waiver of the missed RMD penalty as follows.
From 5329 instructions:
Waiver of tax.
The IRS can waive part or all of this tax if you can show that any shortfall in the amount of distributions was due to reasonable error and you are taking reasonable steps to remedy the shortfall. If you believe you qualify for this relief, attach a statement of explanation and file Form 5329 as follows.
1. Complete lines 52 and 53 as instructed.
2. Enter “RC” and the amount you want waived in parentheses on the dotted line next to line 54. Subtract this amount from the total shortfall you figured without regard to the waiver, and enter the result on line 54.
3. Complete line 55 as instructed. You must pay any tax due that is reported on line 55.
The IRS will review the information you provide and decide whether to grant your request for a waiver.
(The waiver would only be denied if there is no reasonable explanation and the missed RMD was not taken at all.)
You can download the 2015 5329 form from the IRS.
Enter 5329 in the find box and download the 2015 5329 form and instructions.
https://apps.irs.gov/app/picklist/list/priorFormPublication.html
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