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You didn’t actually pay the tax or the 10% penalty (you pay a 10% early withdrawal penalty if you are under 59 ½). You had taxes withheld like from your paycheck. You still have to enter the whole gross amount (before taxes were withheld) with your other income to figure out the total tax (and it may put you into a higher tax bracket) and then the withholding is subtracted from the total tax to figure your refund or tax due. The Gross amount shows up on 1040 line 4a or 5a and the taxable amount on 4b/5b. You will get credit for the withholding on 1040 line 25b.
It has to break out and show the 10% penalty separately on your return (schedule 2 line 8 which goes to 1040 line 23). Then you get credit for all the withholding taken out on 1040 line 25b.
You will pay a 10% oenalty and you will pay tax on the money you took out.
Any withholding is an estimate. The actual tax is calculated on your tax return, based on all your income, credits, and deductions, along with any penalties. You will receive a 1099-R, you must report it. You will get credit for the withholding. If, after all calculations, you owe more, you will pay, and if you owe less than your withholding, you will get a refund.
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