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If you neglected to enter a 1099R on your tax return, then you should not be surprised that the IRS says you owe tax due. When you take money out of a retirement account before you are 59 1/2 there is a 10% early withdrawal penalty and ordinary income tax on the money you took out. The plan should have withheld some tax when you took the money out, but that would only be an estimated amount, just like when an employer withholds money for tax and puts it on a W-2. It all gets entered on your tax return and then the amount of income you received and the amount of tax withheld must be reconciled to see if you owe more or get a refund.
You can amend to see if the amount owed is the same as the amount the IRS is telling you that you owe.
See this TurboTax support FAQ for amending a tax return - https://ttlc.intuit.com/turbotax-support/en-us/help-article/tax-return/amend-change-correct-return-a...
To enter your retirement income, Go to Federal> Wages and Income>Retirement Plans and Social Security>IRA 401 k) Pension Plan Withdrawals to enter your 1099R.
if you add the 1099-R, Turbotax will likely show a lower balance due than the IRS. Their bill includes a penalty for late payment and interest to a certain date. Turbotax does not calculate this penalty or interest.
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