Is HSA contribution already deducted from w2 box1?

Is the HSA contribution amount already deducted from the w2 box 1 federal wages? (If not how do I deduct it from my total taxable income?)

 

Is the additional 0.9% medicare tax also already deducted from w2 box 1?

 

Are IRA and 401k contributions also already deducted from w2 box 1?

 

Thanks.