My wife's made 403b, HSA contributions and medical premium deductions in 2019. However other than the 403B amount no other amounts are deducted from her gross income on lines 3 and 5. All are shown in Line12 with the appropriate codes. All I read on this subject and compared to my W2 tells me these should be deducted from the gross income and lower the income amount shown on line 1 of the W2. Is there a reason for this or is this an error. Looking back through previous years this is the same situation for both 2018 and 2017 as well. Because of the way they are on the W2 I can't make them deductible without overriding what the W2 says which seems incorrect. I just don't think this is correct but I am not an expert and perhaps there is a reason this particular company does it this way.
The way that HSA contributions made through the employer work is that HSA contributions are deducted from Wages in boxes 1, 3, and 5 on your W-2. Since they are removed from all three boxes, you have no way of telling if the employer did this or not (unlike the contribution to a 401(k) plan which is removed only from box 1),
The only way you can determine if your employer removed the HSA contributions from Wages in boxes 1, 3, and 5 on your W-2 is to contact your payroll or HR department and ask them.
The same is true of your premiums for health coverage made through your employer.
If your employer confirms that these amounts were removed from Wages in boxes 1, 3, and 5 on your W-2, then you do not need to deduct them on your return, because they were already removed from income when your W-2 was printed.
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