Your wife's HSA contributions, if they are part of an employer "cafeteria plan" would be exempt from both Federal taxes and Social Security, so it wouldn't be in box 3. See page 11 of these instructions:<a rel="nofollow" target="_blank" href="
https://www.irs.gov/pub/irs-pdf/iw2w3.pdf">https://www.irs.gov/pub/irs-pdf/iw2w3.pdf</a>
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