Next generation sequencing (NGS) technology is playing an increasingly important role in the diagnosis of genetic diseases. Whole exome sequencing (WES) which targets the coding regions of the genome has been widely used in the diagnosis of genetic diseases for its low cost and high efficiency. However, compared to conventional methods, the NGS process is intricate, and there is variability in the expertise of data analysts and variant interpreters, which may lead to inconsistencies in the outcomes. To ensure the quality of testing and enhance the diagnostic rate of diseases, this consensus has provided recommendations regarding the laboratory setup, operational procedures, data analysis, result interpretation, and quality control for WES, with an aim to standardize its application in the detection of genetic disorders.