I used the desktop computer version of TurboTax. I have variable income over the year, so sometimes my estimated tax payments haven't met with IRS requirements. I have noticed that TurboTax calculates the penalty, but doesn't tell you about it; and I seem to recall one year when I got some warning info after running the "error check" before filing, but this kind of processing seems to change every year. Now I have learned the rules, and use form 2210 to calculate the estimated taxes based on my estimated income by quarter. In any case, TurboTax should do the penalty calculations and at least warn you before submission.
