bought $5500 nondeductible traditional ira for 2013 tax year, 8606 form was
submitted by turbo tax back then. In 2016 I converted it to roth ira, the
investment company sent me the 1099R,box1 showed "$5690" and box 7
showed code "2" with ira/sep/simple box "checked". I
followed instruction to fill in this year's Turbo tax (wage/income session),
filled base of $5500 and "0" in value of traditional ira on Dec 31,
2016. So before I click the efile button at the last step, where can I confirm
the tax was only charged from the difference of $5690-$5500(base)? "
Sounds like you did everything correctly. You can verify it by looking at page 1 of your 1040, lines 15a & 15b. Line 15a should have the gross distribution of $5690, and 15b (amount taxable) should have only the $190 difference.