The 1099-R should have been reported on your 2015 tax return. When you follow the 1099-R interview, in TurboTax (TT), the box 1 amount would show on line 15a of form 1040 (line 11a on 1040A) and zero as the taxable amount on line 15b.
Since your bottom line will not change, a letter back to the IRS, explaining the circumstances should be adequate. If you do need to amend; it will be 2015.
