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Earthquake early warning systems are crucial for protecting areas that are subject to these natural disasters. An essential part of these systems is the detection procedure. Traditionally these systems work with seismograph data, but high rate GNSS data has become a promising alternative for the usage in large earthquake early warning systems. Besides traditional methods, deep learning approaches have gained recent popularity in this field, as they are able to leverage the large amounts of real and synthetic seismic data. Nevertheless, the usage of deep learning on GNSS data remains a comparatively new topic. This work contributes to the field of early warning systems by proposing an autoencoder based deep learning pipeline that aims to be lightweight and customizable for the detection of anomalies viz. high magnitude earthquakes in GNSS data. This model, DetEQ, is trained using the noise data recordings from nine stations located in Chile. The detection pipeline encompasses: (i) the generation of an anomaly score using the ground truth and reconstructed output from the autoencoder, (ii) the detection of relevant seismic events through an appropriate threshold, and (iii) the filtering of local events, that would lead to false positives. Robustness of the model was tested on the HR GNSS real data of 2011 Mw 6.8 Concepcion earthquake recorded at six stations. The results highlight the potential of GNSS based deep learning models for effective earthquake detection.