Ah, the old "pass-through". That's important to know.
Let's make some assumptions (you can tell me if they are true or not):
1. When the "pass-through" premiums are sent to your HSA administrator, they appear in box 12 with a code of DD. Thus, they are removed from Wages box 1 just like regular insurance premiums.
2. Any HSA contributions that you made by payroll deduction were also removed from Wages (somehow). Did you make any by payroll deduction?
To enter your contributions, go into the HSA interview. When you get to the screen, "Did your employer tell you about any other contributions?", answer YES.
Three new lines will appear. On the bottom line it reads, "Employer and payroll contributions not reported in box 12 of your W-2". Enter the total contributions (from box 2 on the 5498-SA) here.
This works ONLY if your employer removed all HSA contributions from Wages in Box 1 on your W-2. If this is done right, it will not change your tax due or refund, but will make your paperwork right.
NOTE: a funny thing is that your insurance premiums (code DD in box 12) are removed from Wages, but only from Wages. Employer contributions and your contributions through payroll deductions (code W in box 12) are removed from Wages in boxes 1, 3, and 5. So the result is that when your employer (or you, whoever is paying your health insurance premiums) sends money to the insurance company who then sends some of it to your HSA, that because it is reported with code DD instead of code W, you end up paying Social Security and Medicare tax on the amount of the pass-through.
"From my insurance brochure..." All the things said here are true. The HSA is one of the best deals tax-wise in town, because not only are your contributions tax-free, but also all of your earnings, and so long as you use the money taken out for qualified medical expenses, it will stay tax-free even as you spend it. Smart people use the as a special savings account for when they retire, because you can pay for things like Medicare premiums which you normally can't deduct because the Standard Deduction is so high.
"the contribution by the insurance company that comes out of my premium is not tax deductible." On the contrary, it IS tax-free, if it was part of the code DD amount.
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