Premixed, spark ignited combustion of lean methane at fuel to air equivalence ratio of 0.58 is numerically investigated in a piston-cylinder assembly. The simplified numerical configuration is tailored to emulate the intake, compression and spark ignition processes in engines. Large-eddy simulation is employed in the core flow along with a zonal hybrid wall treatment in near-wall regions. The G-equation level-set method is used to simulate flame propagation with a detailed chemistry based laminar flame speed correlation developed herein. The main numerical findings of this paper are as follows: (1) Despite the geometrical simplicity, the present setup is shown to exhibit relatively large cycle-to-cycle variation for the three investigated cycles. (2) The local thermodynamics and fluid dynamic conditions around the spark close to the ignition location initiate the first discrepancies between the cycles. (3) These early variations are then amplified due to the subsequent differences in the early growth of flame area. (4) The cycle-to-cycle variation in the present set-up is shown to be largely a consequence of the local flow fluctuations close to the spark position and timing, while the results indicated a less dominating role of thermal stratification on cycle-to-cycle variation. (5) The asymmetric combustion behavior was explained to be a combined effect of burning rate and convection velocity, while convection velocity proved to be the major contributor. (6) Finally, a numerical test in the present model setup indicated large spark kernels being less prone to cycle-to-cycle variations than small kernels.