Being able to reliably assess not only the \emph{accuracy} but also the \emph{uncertainty} of models' predictions is an important endeavour in modern machine learning. Even if the model generating the data and labels is known, computing the intrinsic uncertainty after learning the model from a limited number of samples amounts to sampling the corresponding posterior probability measure. Such sampling is computationally challenging in high-dimensional problems and theoretical results on heuristic uncertainty estimators in high-dimensions are thus scarce. In this manuscript, we characterise uncertainty for learning from limited number of samples of high-dimensional Gaussian input data and labels generated by the probit model. In this setting, the Bayesian uncertainty (i.e. the posterior marginals) can be asymptotically obtained by the approximate message passing algorithm, bypassing the canonical but costly Monte Carlo sampling of the posterior. We then provide a closed-form formula for the joint statistics between the logistic classifier, the uncertainty of the statistically optimal Bayesian classifier and the ground-truth probit uncertainty. The formula allows us to investigate calibration of the logistic classifier learning from limited amount of samples. We discuss how over-confidence can be mitigated by appropriately regularising.