The
5498-SA is what your HSA plan administrator reports as contributions.
Your W-2 reports in box 12 with a code of "W" on what your employer contributed and what you contributed through a salary reduction/payroll deduction plan.
First, did you make any contributions to your HSA outside of your employer (like send the HSA plan administrator a check directly)? If so the 5498-SA should be different from the W-2, because the 5498-SA includes both W-2 numbers and your outside contributions.
If, however, the W-2 failed to include a $50 amount that your employer contributed (and you see it on the 5498-SA), then your employer owes you a corrected W-2.
When you get the corrected W-2, amend your return.
Otherwise, the IRS may notice the discrepancy and send you a letter. To help prod your employer, remind them that contributions to and distributions from your HSA are taxable if they are not reported on your 8889 - in this case, with the $50 missing from your W-2, it is also missing from your 8889 and the IRS will consider that $50 taxable (and it shouldn't be).
