Box 12 (a, b, c or d) should indeed have $5,000 with a "W" in front of it, assuming it is indeed an HSA. (Since you have both employer & employee contributions, it's not likely to be some other kind of medical account such as an HRA or FSA.) You do say, however, that there's something in Box 12. Does it have a letter code in front of it? Is it employer AND pre-tax employee contributions combined (correct), employee contributions only (incorrect), or HDHP premiums (incorrect unless the letter code is "DD", i.e., non-taxable value of employer-provided health insurance)?
Edit: Note that $5,000 exceeds the limit on HSA contributions for an individual. Are you sure this is an HSA and *not* an HRA, FSA or other medical account? Do you have family coverage on your HDHP, which would raise the limit above $5,000?
