The Lupus Foundation of America states, "The immunofluorescent antinuclear antibody (ANA or FANA) test is positive in almost all individuals with systemic lupus (97 percent), and is the most sensitive diagnostic test currently available for confirming the diagnosis of systemic lupus when accompanied by typical clinical findings." So my inclination is that it is relatively rare. Having said that, You could certainly be one of those rare cases.
I've been diagnosed with Lupus, but am changing rheumatologists. I've seen another in the past who said I definitely did not have Lupus, but had Sjogren's. Then two months later I was told that I do not have Sjogren's, but do have Lupus. I'm going for a third opinion (primarily because I do not trust the second and the first does not take my insurance) I say, keep trying to figure all of this out. Lupus symptoms come and go for many of us. I've had a positive ANA for at least 10 years, but was never considered to have anything other than FMS until last September. Good luck and keep us posted!