Pathogenicity predictions offered by HmtVar are calculated using specific pathogenicity criteria.

Pathogenicity predictions are offered for non-synonymous and tRNA variants based on disease score and allele frequency values, as further detailed in the related pages.

Non-synonymous CDS variants

Tier Disease Score range Allele Frequency range
Polymorphic DS < 0.43 AF > 0.003264
Likely Polymorphic DS < 0.43 AF ≤ 0.003264
Likely Pathogenic DS ≥ 0.43 AF > 0.003264
Pathogenic DS ≥ 0.43 AF ≤ 0.003264

tRNA variants

Tier Disease Score range Allele Frequency range
Polymorphic DS < 0.35 AF > 0.005020
Likely Polymorphic DS < 0.35 AF ≤ 0.005020
Likely Pathogenic DS ≥ 0.35 AF > 0.005020
Pathogenic DS ≥ 0.35 AF ≤ 0.005020