It sounds like you are stuck in the "gap" between the IRS's automated correction and the manual requirements of an amended return. To clarify the process and help you find that missing "error" in you...
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It sounds like you are stuck in the "gap" between the IRS's automated correction and the manual requirements of an amended return. To clarify the process and help you find that missing "error" in your net profit, here is the breakdown:
1. The AGI and the "Error" in Net Profit (Schedule C)
To answer your second point: No, TurboTax will not automatically update your AGI based on the IRS transcript. TurboTax is a static calculator; it only knows what you type into it.
The IRS stated your "computation of net profit or loss was in error." This refers to Schedule C. Since your AGI changed, it means the IRS changed your Taxable Income, likely by adjusting one of these three things:
Math Error: You may have simply added or subtracted your expenses incorrectly on Schedule C.
Self-Employment Tax: If your Net Profit changed, your Self-Employment tax (and the subsequent 50% deduction of that tax on your 1040) also changed.
Transcription Error: You might have carried a number from Schedule C to Schedule 1 incorrectly.
How to find it: Compare your original Schedule C, Line 31 (Net Profit) to the IRS transcript line that says "Business Income" or "Statutory Profit/Loss." If those numbers are different, that is your "Error." You must manually go into the "Business Income" section of TurboTax and adjust your income or expenses until the Net Profit matches the IRS’s number. Once that matches, your AGI will automatically fix itself.
2. Where to report the Roth/IRA changes (Form 1040-X)
Regarding your question about where this goes on the paper form (Form 1040-X:(
The AGI Change: This goes in Part I, Line 1.
Column A: Original AGI you filed.
Column B: The amount of the increase or decrease.
Column C: The new AGI (matching the IRS transcript).
The Roth Contribution/Recharacterization: * Roth contributions themselves are not reported on Form 1040-X because they aren't tax-deductible.
However, if you exceeded the income limit and had to move the money to a Traditional IRA (recharacterization) or withdraw it, you must explain this in Part III (Explanation of Changes) on page 2.
You would write: "AGI was adjusted by the IRS from [Old AGI] to [New AGI]. Due to this increase, my MAGI exceeded the threshold for Roth IRA contributions. I have [recharacterized/withdrawn] the excess contribution of $[Amount] plus earnings."
3. MAGI vs. AGI for Roth Purposes
You mentioned you "guessed" that MAGI and AGI were the same. For most people, they are very close, but for a self-employed person, they can differ.
MAGI for Roth purposes is your AGI before you take the deduction for the "student loan interest" or "tuition and fees," but after you take the deduction for one-half of your self-employment tax.
If you are using TurboTax, the software will calculate your MAGI for you once you fix the Schedule C error. Look for the "IRA Contribution Merit" or "Roth Contribution" worksheet in your "Forms Mode" to see the exact MAGI number the software is generating.
Summary of your next steps:
Fix Schedule C: In TurboTax, edit your business expenses/income until your Net Profit matches the IRS transcript.
Verify AGI: Check that your New AGI in TurboTax matches the "Adjusted Gross Income" line on the IRS transcript.
Adjust IRA: Go to the "Deductions & Credits" section, select "IRA Contributions," and enter the information about your Roth contribution. The software will tell you if you are over the limit based on the new AGI.
Explain in Part III: In the 1040-X "Explanation of Changes" section, clearly state that you are amending to reconcile your records with the IRS CP2000 (or other notice) adjustment and to address the resulting excess Roth contribution.