For contemporary software systems, security is considered to be a key quality factor and the analysis of IT security risk becomes an indispensable stage during software deployment. However, performing risk assessment according to methodologies and standards issued for the public sector or large institutions can be too costly and time consuming. Current business practice tends to circumvent risk assessment by defining sets of standard safeguards and applying them to all developed systems. This leads to a substantial gap: threats are not re-evaluated for particular systems and the selection of security functions is not based on risk models. This paper discusses a new lightweight risk assessment method aimed at filling this gap. In this proposal, Fuzzy Cognitive Maps (FCMs) are used to capture dependencies between assets, and FCM-based reasoning is performed to calculate risks. An application of the method is studied using an example of an e-health system providing remote telemonitoring, data storage and teleconsultation services. Lessons learned indicate that the proposed method is an efficient and low-cost approach, giving instantaneous feedback and enabling reasoning on the effectiveness of the security system.