After you have entered the information reported on your Form 1099-R, one of the follow-up questions should ask about your basis in the account, or any non-deductible contributions that were made to the account.
If you did not see that as part of the follow-up questions, you can also enter the basis of an IRA in the Deductions and Credits > Retirement and Investments > Traditional and Roth IRA Contributions section of your return.
As you get started in that section, check the box for the type of IRA you have and go through the screens until you see a question about 'any non-deductible contributions' to your IRA. Check 'yes' and then enter the total basis of the account. Remember, this is only asking for the contributions that were made, not the total value of the IRA.
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