We are happy to announce a manuscript that describes our pipeline to call mitochondrial DNA variants in gnomAD v3, released in November 2020. This paper details the pipeline and extensive filtering required to achieve a high quality call set, with particular emphasis on avoiding false positives due to misalignment. It explores the mitochondrial variation across 56,434 individuals, including allele frequencies, carrier rates, comparison of mitochondrial versus nuclear ancestry, and patterns of variation in mitochondrial genes.