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Dear Brass Tax Presentations,
We amended a 2019 Form 1040 from MFS to MFJ. The original return was e-filed on 3/28/22, and amended on 3/18/24 (within the 3 years). However, the IRS rejected the refund request because the amendment was “filed late”, that it is 3 years from the due date, not 3 years from the original filing of the return. Can you clarify? I looked it up in many ways, but I keep seeing 3 Yrs from the original filing date. Is it a special case when amending the return from MFS to MFJ?
Thanks.
From Brass Tax Presentations
You are correct that the refund statute is the later of three years from the date the return was filed (or two years from the date the tax was paid, whichever is later), but a few key components are coming into play here.
Since the original return was filed late, the three-year statute begins on the date the return was filed, however, the code states that the amount refunded will be limited to the amount that was paid within the three-year period preceding the claim. You can take a look at IRC Section 6511(b)(2)(A).
Withholding and any estimated payments are treated as having been paid when the return was due, so withholding from 2019 wages would be treated as having been paid on the due date of the return in 2020. This was decided by the Supreme Court in Baral v US.
With the fact pattern that you described, unless there was some additional tax paid with the filing of the original MFS returns, it does sound like that amendment was out of statute for the refund.