mvTool v.5 - Universal mtDNA Variant Converter and One Stop Annotation

Input mtDNA Variants in Any of the 7 Formats Below, Mixed Formats Input is Supported:

in reference to in rCRS.

To check new variant entries, press "Convert" or "Annotate" button. We recommend running HGVS format check if the result is not as expected.

Mitochondrial DNA variant nomenclature has multiple existing systems used in literature and in different institutes. The major ways are:

1. Classical I: used in literature, PhyloTree, Haplogrep, 8527, 8993G, 8993d, 5787_5789d, 1494.1T, 7472.XA
2. Classical II: T8993G
3. HGVS Committee: NC_012920.1:m.8993T>G, reference version is required. This is the recommended format, being required by journals and NCBI/ClinVar. The short naming like m.8993T>G is also widely used in literature, assuming rCRS as reference.

4. VCF-style input: Tab-delimited, with at least the first 5 columns in vcf format
5. Ensembl: MT:g.8993T>G
6. Mutalyzer: NC_012920.1:g.8993T>G
7. Potential non-standard: 8527A>G

mvTool supports the chromosome names as any of the following:
chrM, chM, chrMT, chMT, M, MT, NC_012920.1.

The mvTool universal variant converter can convert the various combinations of these formats into a standard variant list in the rCRS-based HGVS (1-3) formats.

The current mtDNA variant data is mostly based on the default revised Cambridge sequence (rCRS, accession number NC_012920.1). The use of YRI (Yoruban, accession number NC_001807.4, derived from AF347015) as the mitochondrial reference genome is discouraged by NCBI. Since some commercial SNP array platforms used or may still use YRI as the reference genome, mvTool can convert YRI-based positions into rCRS-based positions, but only for backward compatibility. The mvTool does not covert rCRS coordinates to YRI-based coordinates.

Annotate both mtDNA and nuclear DNA variants? Switch to One-Stop Variant Annotation.
Novel pathogenic variant? Please submit.

*Disclaimer: This mvTool and associated data are strictly for research purpose only, they are not clinically-validated nor applicable for clinical diagnosis.

The major mvTool collaborators and data sources:
MSeqDR Logo Mitomap  MitoTIP tRNA Scoring     dbNSFP   HmtDB Ensembl PhyloTree GeneDX Inc. OMIM ClinVar uman-phenotype-ontology