Logic behind ACMG classification of SNVs

The SNVs classification engine applies the joint American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines for interpreting sequence variants using 28 evidence criteria (PMID: 25741868).

Emedgene independently determines the overall ACMG variant pathogenicity score and class.

ACMG variant classification

Emedgene applies the ACMG classification guidelines for variant interpretation using the standardized framework established by the American College of Medical Genetics and Genomics (ACMG). This approach is further refined with recommendations from the ClinGen Sequence Variant Interpretation (SVI) Working Group and other expert-reviewed publications to ensure consistent, evidence-based classification of genomic variants.

When assigning a final classification, Emedgene applies the ACMG thresholds with the above combination rules:

Pathogenic

• 1 Very Strong (PVS1) and ≥1 Strong (PS1–PS4), or

• 1 Very Strong and ≥2 Moderate (PM1–PM6), or

• 1 Very Strong + 1 Moderate + 1 Supporting, or

• 1 Very Strong + ≥2 Supporting (including PM2), or

• ≥2 Strong, or

• 1 Strong + ≥3 Moderate, or

• 2 Moderate + ≥2 Supporting, or

• 1 Moderate + ≥4 Supporting.

Likely Pathogenic

• 1 Very Strong + 1 Moderate, or

• 1 Very Strong + 1 Supporting, or

• 1 Strong + 1–2 Moderate, or

• 1 Strong + ≥2 Supporting, or

• ≥3 Moderate, or

• 2 Moderate + ≥2 Supporting, or

• 1 Moderate + ≥4 Supporting.

Benign

• 1 Stand-alone benign (BA1) — overrides all other tags, or

• ≥2 Strong benign (BS1–BS4).

Likely Benign

• 1 Strong benign + 1 Supporting benign, or

• ≥2 Supporting benign (BP1–BP7).

ACMG variant score

Emedgene calculates the ACMG score for Single Nucleotide Variants (SNVs) using the framework recommended by the American College of Medical Genetics and Genomics (ACMG), along with refinements from ClinGen Sequence Variant Interpretation (SVI) Working Group and other published guidelines (PMID: 32720330).

The software assigns points to each active criterion based on its strength of evidence:

• Supporting evidence = 1 point

• Moderate evidence = 2 points

• Strong evidence = 4 points

• Stand-alone or Very Strong evidence = 8 points

The total ACMG score is calculated by adding the points from all pathogenic criteria and subtracting the points from all benign criteria. The result is then interpreted according to these thresholds:

For mtDNA variants, the software excludes the following tags from class calculation: PM1, PM3, PP2, PP5, BP1, BP3, and BP6.

Tag strength adjustments and combination rules

Some ACMG criteria have special handling to ensure consistent scoring in line with expert recommendations:

• PM2 always counts as Supporting strength, regardless of any manual user change (PM2 SVI Recommendation Ver 1.0, 2020). If you set PM2 to a higher level, the system will warn:

Warning: PM2 is recommended to be set to supporting level (PM2 SVI Recommendation Ver 1.0, 2020)

• If Very Strong (PVS1) is combined with any Supporting (PP1–PP5), the maximum final classification is Likely Pathogenic, not Pathogenic (PM2 SVI Recommendation Ver 1.0, 2020).

• If PM1 and PP3 are both positive, the combination is capped at Strong strength, regardless of individual strengths (Pejaver et al., 2022). This prevents inflated scoring when computational evidence overlaps with known mutational hotspot data.

• PP5 (pathogenic from reputable source) and BP6 (benign from reputable source) are excluded from final score calculation (Biesecker et al., 2018). These can still be displayed for reference but will not affect the classification.

• Double-counting prevention rules:

  • PVS1 + PP3 → only PVS1 is counted; PP3 is ignored (Abou Tayoun et al., 2018).

  • PVS1 + PM4 → only PVS1 is counted; PM4 is ignored (Abou Tayoun et al., 2018).

  • PS2 + PM6 → only one is counted, depending on whether de novo status is confirmed (ClinGen SVI WG).

Tracking and traceability of manual changes

The interface tracks and displays all manual modifications to ACMG tags, including changes to tag status, strength, or question responses:

• User icon → appears on tags, questions, or strength indicators when manually changed. Hover to see the username.

• Emedgene icon (EMG) → indicates the system’s original automated classification. Hover to see the original status or strength.

• Dependency-driven changes (e.g., a strength auto-adjusted because a related question was changed) still show the user icon for traceability.

• Revert button → restores tags, strengths, and questions to their last saved state (manual or system-generated).

In the Summary tab, tags are color-coded, and manual changes show user icons directly on the tag for quick review.

Real-time warnings during classification

When certain tag combinations are applied, the system displays immediate, context-specific warnings in the header area:

• PM2 changed → “PM2 is recommended to be set to supporting level (PM2 SVI Recommendation Ver 1.0, 2020).”

• PM1 + PP3 both positive → “When PM1 is applied with PP3, the outcome will be limited to Strong (Pejaver et al., 2022).”

• PP5 positive → “PP5 excluded (Biesecker et al., 2018).”

• BP6 positive → “BP6 excluded (Biesecker et al., 2018).”

• PVS1 + PP3 → “PVS1 cannot be counted together with PP3 (Abou Tayoun et al., 2018).”

• PVS1 + PM4 → “PVS1 cannot be counted together with PM4 (Abou Tayoun et al., 2018).”

Tips for users:

• Always review tag strengths before finalizing, especially for borderline LP/P classifications.

• Check for automatic exclusions (PP5, BP6) so you understand why they don’t contribute to scoring.

• Avoid overriding PM2, PM1, or PP3 without justification — the system’s defaults are based on published recommendations.

• Use the activity log to track and audit all manual modifications.

• Pay attention to real-time warnings — they’re designed to prevent misclassification due to known interpretation pitfalls.