I've looked at my W-2s and 5498-SAs for the past 3 years. My W-2 entry is always equal to or a few pennies less than the max HSA contribution allowed for that year (at worse it was 16 cents less). However, my 5498-SA entry is anywhere from about $4 to $16 less than the W-2 entry.
I've seen a number of discussions about this already, but it seems to always relate to either confusion between employer and employee contributions and the W-2 not including employer contributions, or the employee making contributions that were not from payroll deductions. That's not my case. My employer does make a contribution (I think $700) and the rest I contribution through payroll deductions.
I have box 3 entries on my 5498-SA for contributions made in one year that were for the previous tax year. This usually a little over $300, but varies. Here's what I noticed. If you take the difference between a box 3 entry in one year and the next (which is always a small increase), it equals the difference between the W-2 entry and the 5498-SA box 2 entry. So it seems box 2 takes the W-2 entry, subtracts this year's box 3 entry, and adds the previous year's box 3 entry.
I think what happens here is my last HSA payroll deduction of the year is not actually contributed to the HSA until a few days later, which is the start of the next calendar year. So the W-2 says the HSA deduction from the last paycheck was part of the current tax year, but the 5498-SA says it is part of the next tax year. Certainly confusing, but at least I think I understand what is going on now, and I think while typing this up I've answered the question I was going to ask. 😁
