Can the formula F=ma be a direct variation equation? If so, which variable would have to be held constant?

Yes it can be a direct variation. it follows the form y = kx

The only variable that cannot be held constant is F, but we can hold the mass constant and vary the acceleration OR we can hold the acceleration constant and vary the mass. Either one would work, but the easiest would be to vary the mass and hold the acceleration constant since we are all pulled by the same action gravity