You can request an amended 1098-T, so that you can try to get an education credit.
As a graduate student, you might be eligible for the Lifetime Learning Credit, which will give you a 20% credit on the amounts you pay for tuition, fees, books and required supplies, up to a maximum of $2,000. But this is only a credit against taxes that you would otherwise owe, and if you don't owe any tax, you won't get a credit. If you are a four-year student, you may qualify for AOC.
Although the IRS doesn't address your particular situation directly, it is quite clear that any payments for services rendered by a student at a college or university are taxable. The IRS goes on to say that students are exempt from FICA tax.
Other colleges and universities specifically address your situation. UW-Madison, for instance, says RA wages are fully taxable, and taxes will be withheld.
Columbia University describes stipends as payments for room and board that may be taxable to the student but are not reported to the IRS. Payments for services rendered are taxable wages, and taxes will be withheld.
In reporting your room and board in box 5, the university may be doing you a favor.
Because you haven't revealed the rest of your income, it's impossible to tell from this perspective whether it is better for you to leave well enough alone, or to insist that the school correct the 1098-T.
Based upon what the IRS says, your stipend should be subject to income tax but not FICA. If you have no other income, there would be no advantage to you to change the 1098-T, as you would not owe any tax and therefore would not be eligible for an education credit. If you earned another $10,000 during the summer, without changing the 1098-T, you would still owe no tax, because you haven't exceeded the filing requirement. Only if your taxable earnings (in addition to this stipend) exceed $10,400 would changing the 1098-T make a difference to you.
If you don't have more than $10.400 in other taxable earnings, I would leave well enough alone.
