As a computationally efficient framework, the random matrix approach can simultaneously estimate the kinematic state and extent of the extended target. For the extended target tracking in clutter, the measurement origin uncertainty, the unknown detection probability and measurement rate challenge the existing methods. In this paper, we propose the Beta Gamma Gaussian inverse Wishart filter based on the variational approximation. The proposed method takes the association event as an unknown parameter with a prior distribution. Following a more rigorous path, we derive an approximate posterior distribution of the unknowns using the analytical techniques of variational Bayesian inference. The joint estimations of the kinematic state, extent, detection probability, measurement rate and association events are obtained in this work. The simulation results illustrate the effectiveness and robustness of the proposed approach.