The IRA/SEP/SIMPLE box not being marked on the Form 1099-R provided by the payer indicates that the annuity is not an IRA annuity (unless the payer prepared the form incorrectly, which is unlikely) and is not to be included anywhere on Form 8606. Perhaps the annuity is in some other kind of qualified retirement account such as a pension or an annuity in the federal TSP. However, if box 7 of the Form 1099-R includes code D, it indicates that it is a nonqualified annuity.
If box 2a of this Form 1099-R without the IRA/SEP/SIMPLE box marked shows an amount and box 2b Taxable amount not determined is not marked, that's the amount that the IRS will expect to see included on Form 1040 line 4d unless explanation is provided as to why this amount is incorrect. If box 2a is blank and box 2b Taxable amount not determined is marked, the taxable amount must be determined using the Simplified Method or the General Rule depending on whether the annuity is a qualified or nonqualified annuity.
