In some cases, it is easier to use the TurboTax interview questions. Testing this put the correct taxable amount on Line 3 of Form 8960.
Is a Taxable Amount showing in Box 2a on your 1099-R? Either the Form 1099-R will show the taxable amount in box 2a or it is blank with 'taxable amount not determined' indicated.
If this applies, you may need to use use your annuity statements to determine the basis.
Non-qualified annuities are typically purchased with after-tax money; generally only the Earnings are taxable.
Click this link for more info on Non-Qualified Annuities.
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