Within the EU-FP7 SARNET2 project a Generic Containment nodalisation, based on a German PWR (1300 MWe), was developed and used in the benchmark exercise in order to compare simulations performed with various codes using the same nodalisation. The recommendation to elaborate such Generic Containment concept was one of the outcomes of the OECD/NEA ISP-47 activity to allow comparison of the results obtained by different lumped-parameter models on plant scale. Even though the model of the Generic Containment and the transient scenario were precisely and uniquely defined, very different results were obtained not only between different codes but also between participants using the same code, showing that the "user-effect" can have significant influence on the results. The aims of this work are to estimate an uncertainty related to the conditions of the simulated transient and nodalisation choices, e.g., initial temperature, material properties, junction parameters, etc., and compare it to the "user-effect" related uncertainty obtained in the SARNET2 project. The paper presents uncertainty estimation using the GRS method for uncertainty and sensitivity evaluation and obtained results in the context of the "user-effect" uncertainties.