Why is there a $3000 discrepancy between my estimated refund and what was direct deposited?

Is the amount sent/issued by the IRS the same as the refund amount shown on your federal tax return Form 1040 Line 35a? - https://www.irs.gov/refunds

If not, then go to this IRS website for information on reduced refunds - https://www.irs.gov/taxtopics/tc203