The rapid increase of the number of objects in orbit around the Earth poses a serious threat to operational spacecraft and astronauts. In order to effectively avoid collisions, mission operators need to assess the risk of collision between the satellite and any other object whose orbit is likely to approach its trajectory. Several algorithms predict the probability of collision but have limitations that impair the accuracy of the prediction. An important limitation is that uncertainties in the atmospheric density are usually not taken into account in the propagation of the covariance matrix from current epoch to closest approach time. The atmosphere between 100 km and 700 km is strongly driven by solar and magnetospheric activity. Therefore, uncertainties in the drivers directly relate to uncertainties in the neutral density, hence in the drag acceleration. This results in important considerations for the prediction of Low Earth Orbits, especially for the determination of the probability of collision. This study shows how uncertainties in the atmospheric density can cause significant differences in the probability of collision and presents an algorithm that takes these uncertainties into account to more accurately assess the risk of collision. As an example, the effects of a geomagnetic storm on the probability of collision are illustrated.