Did you have excess contributions? How were the HSA contributions made? Through your employer or directly to the HSA custodian?
One often confusing thing is that the HSA contributions through payroll deduction (which are reported in box 12 with a code of W on your W-2) are removed from Wages in boxes 1, 3, and 5. This is the tax benefit - the contributions are never in your income. This is why the code W amount doesn't appear as a deduction anywhere, it doesn't need to. Does this describe your situation?
@Va18
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