For reliable and efficient network planning and operation, accurate estimation of Quality of Transmission (QoT) before establishing or reconfiguring the connection is necessary. In optical networks, a design margin is generally included in a QoT estimation tool (Qtool) to account for modeling and parameter inaccuracies, ensuring the acceptable performance. In this work, we use monitoring information from an operating network combined with supervised machine learning (ML) techniques to understand the network conditions. In particular, we model the penalties generated due to i.) Erbium Doped Fiber Amplifier (EDFA) gain ripple effect, and ii.) filter spectral shape uncertainties at Reconfigurable Optical Add and Drop Multiplexer (ROADM) nodes. Enhancing the Qtool with the proposed ML regression models yields estimates for new or reconfigured connections that account for these two effects, resulting in more accurate QoT estimation and a reduced design margin. We initially propose two supervised ML regression models, implemented with Support Vector Machine Regression (SVMR), to estimate the individual penalties of the two effects and then a combined model. On Deutsche Telekom (DT) network topology with 12 nodes and 40 bidirectional links, we achieve a design margin reduction of ~1dB for new connection requests.