Discrepancy on how HSA credits calculated

[anonymous2]

on my W2 in 12A I have my pre-tax HSA contributions listed and the form is imported successfully.

However, I get a screen 'Be sure to add HSA info on contributions and credits to get all the tax savings you earned' Also a s help link '
If your HSA contributions weren't included in Box 12 of your W-2, those amounts are deductible because you paid tax on those contributions (there are limits, and we'll be sure to check on those). These contributions lower your overall taxable income at the end of the year, which means you get taxed on less income.'
So what does this all mean. Even though my HSA pre-tax was picked up by TurboTax I still have to enter it later on to get the tax savings. IE those credits are not yet counted toward my refund/owe score?

[Bsch4477]

If your HSA contribution was reflected on your W-2 and you made no additional contribution, TurboTax will handle all of the calculations and you need do nothing more. 

[anonymous2]

except that later in the interview TurboTax is asking me how much was subtracted from my paycheck vs how much was contributed from other sources, how much I used for medical expenses etc. Can I assume that this all ties in together and I am getting the correct final calculation?

thank you

[BillM223]

There are two ways to contribute to your HSA: (1) through your employer (either by the employer or a payroll deduction plan by you), and (2) by a direct contribution from you to your HSA custodian.

#1 appears in box 12 on your W-2 with a code of W and the amount. #2 appears on line 12 on Schedule 1 (1040).

#1 is NOT on line 12 on Schedule 1 because it was removed from Wages in box 1, 3, and 5 on your W-2 when it was printed. So it's not a deduction on your return because it was never in your income in the first place.

On the screen "Let's enter (name)'s HSA contributions" do NOT enter any part of the code W amount on the second line! Enter on this line only amounts you sent directly to your HSA custodian (not through your employer).

So, as Bsch4477 said, enter your code W amount with your W-2 and any direct contributions on the "Let's enter (name)'s HSA contributions" on the second line, and TurboTax will take care of the rest.