The penalty on early distributions from your Roth IRA account only applies to the earnings portion of the distribution. It does not apply to the amounts that you have contributed.
After you have entered your form 1099-R, TurboTax will take you back to the summary page titled Your 1099-R Entries.
On that page, click Continue and follow the TurboTax until you arrive at the page titled Enter Prior Year Roth IRA Contributions where you can enter the amount of your past contributions.
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