The 10% deduction on your withdrawal are taxes withheld, and not the 10% early withdrawal penalty.
Tax withheld is just an estimated advance payment of your taxes. The final tax amount can only be determined when you fill out your tax return. The taxes withheld serve as a credit against your tax liability. If too much tax was withheld, you'll receive a refund; otherwise, there'll be a tax due.
You have to enter that form 1099-R on your tax return.
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