The development of fragility curves to perform seismic scenario-based risk assessment requires a fully probabilistic procedure in order to account for uncertainties at each step of the computation. This is especially true when developing fragility curves conditional on an Intensity Measure that is directly available from a ground-motion prediction equation. In this study, we propose a new derivation method that uses realistic spectra instead of design spectral shapes or uniform hazard spectra and allows one to easily account for the features of the site-specific hazard that influences the fragility, without using non-linear dynamic analysis. The proposed method has been applied to typical school building types in the city of Basel (Switzerland) and the results have been compared to the standard practice in Europe. The results confirm that fragility curves are scenario dependent and are particularly sensitive to the magnitude of the earthquake scenario. The same background theory used for the derivation of the fragility curves has allowed an innovative method to be proposed for the conversion of fragility curves to a common IM (i.e. spectral acceleration or PGA). This conversion is the only way direct comparisons of fragility curves can be made and is useful when inter-period correlation cannot be used in scenario loss assessment. Moreover, such conversion is necessary to compare and verify newly developed curves against those from previous studies. Conversion to macroseismic intensity is also relevant for the comparison between mechanical-based and empirical fragility curves, in order to detect possible biases.