We present magnetotransport data on the ferrimagnet GdMn$_6$Sn$_6$. From the temperature dependent data we are able to extract a large instrinsic contribution to the anomalous Hall effect $sigma_{xz}^{int} sim$ 32 $Omega^{-1}cm^{-1}$ and $sigma_{xy}^{int} sim$ 223 $Omega^{-1}cm^{-1}$, which is comparable to values found in other systems also containing kagome nets of transition metals. From our transport anisotropy, as well as our density functional theory calculations, we argue that the system is electronically best described as a three dimensional system. Thus, we show that reduced dimensionality is not a strong requirement for obtaining large Berry phase contributions to transport properties. In addition, the coexistence of rare-earth and transition metal magnetism makes the hexagonal MgFe$_6$Ge$_6$ structure type a promising system to tune the electronic and magnetic properties in future studies.
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