Non-invasive prenatal testing as a valuable source of population specific allelic frequencies

•Low-coverage WGS based NIPT is a low-cost test rapidly adopted around the globe.•We re-used NIPT data for population specific frequency determination of DNA variants.•For this we used aggregation of reads from a large cohort of individuals.•Different lines of evidence suggested reliability of detected variant frequencies.•Our approach can improve generation of population specific genomic reference data sets.