Use practical formula from ASHRAE Fundamentals to calculate it:
p,st = 0,192 x (ro,a - ro) x (z2 - z1)
ro,a - ambient air density
ro - supply air density.
You have to care about direction: if you supply cold air upwards (fan is at the bottom) ro > ro,a, stack effect is downwards and will act as additional pressure loss. If you supply warm air in the same direction, stack effect will "help" fan. The opposite applies to downward design flow.
To assess whether is negligible or not, calculate, compare with total pressure drop calculated for system and you will see.
When in doubt, it is much more responsible to check it (as you are seemingly attempting) than to find resort in general "rule of thumb" assumptions.
Rules of thumb are good only if you are certain that you can apply them.