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TurboTax handles such a situation just fine. All you have to do is enter the 1099-R exactly as printed, then answer the questions on the screens that will follow.
When you prepare and file your taxes with TurboTax, if you have correctly answered all questions and entered the form 1099-R, then the 10% early withdrawal has been properly calculated and the refund (or tax due) that you see has already taken into account this penalty.
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