The invention discloses a mitochondrial
DNA variation
pathogenicity evaluation method, and relates to the technical field of variation analysis, and the method comprises the following steps: obtaining mitochondrial
DNA of a to-be-detected suspected
mitochondrial disease patient, carrying out high-
throughput sequencing, quality screening and site comparison on the
DNA, obtaining first VCF file data, screening the first VCF file data, constructing a second variation site set, and determining the
pathogenicity of the mitochondrial DNA variation
pathogenicity of the to-be-detected suspected
mitochondrial disease patient. On the basis of the second variation site set, according to the evaluation standard table, evaluating the mitochondrial DNA variation pathogenicity of the suspected
mitochondrial disease patient, effectively rejecting low-
quality data by combining a three-level quality screening
system with variation site double filtering conditions, providing a high-confidence variation site set for subsequent analysis, and improving the accuracy of the quality of the suspected mitochondrial
disease patient. The mitochondrial
DNA mutation pathogenicity evaluation is more comprehensive and accurate by performing three-level quality screening, multi-
database combined filtering and dynamic scoring mechanism on the mitochondrial DNA.