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The deployment of autonomous systems that operate in unstructured environments necessitates algorithms to verify their safety. This can be challenging due to, e.g., black-box components in the control software, or undermodelled dynamics that prevent model-based verification. We present a novel verification framework for an unknown dynamical system from a given set of noisy observations of the dynamics. Using Gaussian processes trained on this data set, the framework abstracts the system as an uncertain Markov process with discrete states defined over the safe set. The transition bounds of the abstraction are derived from the probabilistic error bounds between the regression and underlying system. An existing approach for verifying safety properties over uncertain Markov processes then generates safety guarantees. We demonstrate the versatility of the framework on several examples, including switched and nonlinear systems.