gh-k-dense-ai-claude-scientific-skills-scientific-skills/skills/clinvar-database/references/clinical_significance.md

ClinVar Clinical Significance Interpretation Guide

Overview

ClinVar uses standardized terminology to describe the clinical significance of genetic variants. Understanding these classifications is critical for interpreting variant reports and making informed research or clinical decisions.

Important Disclaimer

ClinVar data is NOT intended for direct diagnostic use or medical decision-making without review by a genetics professional. The interpretations in ClinVar represent submitted data from various sources and should be evaluated in the context of the specific patient and clinical scenario.

Three Classification Categories

ClinVar represents three distinct types of variant classifications:

1. Germline variants - Inherited variants related to Mendelian diseases and drug responses
2. Somatic variants (Clinical Impact) - Acquired variants with therapeutic implications
3. Somatic variants (Oncogenicity) - Acquired variants related to cancer development

Germline Variant Classifications

Standard ACMG/AMP Terms

These are the five core terms recommended by the American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP):

Term	Abbreviation	Meaning	Probability
Pathogenic	P	Variant causes disease	~99%
Likely Pathogenic	LP	Variant likely causes disease	~90%
Uncertain Significance	VUS	Insufficient evidence to classify	N/A
Likely Benign	LB	Variant likely does not cause disease	~90% non-pathogenic
Benign	B	Variant does not cause disease	~99% non-pathogenic

Low-Penetrance and Risk Allele Terms

ClinGen recommends additional terms for variants with incomplete penetrance or risk associations:

• Pathogenic, low penetrance - Disease-causing but not all carriers develop disease
• Likely pathogenic, low penetrance - Probably disease-causing with incomplete penetrance
• Established risk allele - Confirmed association with increased disease risk
• Likely risk allele - Probable association with increased disease risk
• Uncertain risk allele - Unclear risk association

Additional Classification Terms

• Drug response - Variants affecting medication efficacy or metabolism
• Association - Statistical association with trait/disease
• Protective - Variants that reduce disease risk
• Affects - Variants that affect a biological function
• Other - Classifications that don't fit standard categories
• Not provided - No classification submitted

Special Considerations

Recessive Disorders: A disease-causing variant for an autosomal recessive disorder should be classified as "Pathogenic," even though heterozygous carriers will not develop disease. The classification describes the variant's effect, not the carrier status.

Compound Heterozygotes: Each variant is classified independently. Two "Likely Pathogenic" variants in trans can together cause recessive disease, but each maintains its individual classification.

Somatic Variant Classifications

Clinical Impact (AMP/ASCO/CAP Tiers)

Based on guidelines from the Association for Molecular Pathology (AMP), American Society of Clinical Oncology (ASCO), and College of American Pathologists (CAP):

Tier	Meaning
Tier I - Strong	Variants with strong clinical significance - FDA-approved therapies or professional guidelines
Tier II - Potential	Variants with potential clinical actionability - emerging evidence
Tier III - Uncertain	Variants of unknown clinical significance
Tier IV - Benign/Likely Benign	Variants with no therapeutic implications

Oncogenicity (ClinGen/CGC/VICC)

Based on standards from ClinGen, Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC):

Term	Meaning
Oncogenic	Variant drives cancer development
Likely Oncogenic	Variant probably drives cancer development
Uncertain Significance	Insufficient evidence for oncogenicity
Likely Benign	Variant probably does not drive cancer
Benign	Variant does not drive cancer

Review Status and Star Ratings

ClinVar assigns review status ratings to indicate the strength of evidence behind classifications:

Stars	Review Status	Description	Weight
★★★★	Practice Guideline	Reviewed by expert panel with published guidelines	Highest
★★★	Expert Panel Review	Reviewed by expert panel (e.g., ClinGen)	High
★★	Multiple Submitters, No Conflicts	≥2 submitters with same classification	Moderate
★	Criteria Provided, Single Submitter	One submitter with supporting evidence	Standard
☆	No Assertion Criteria	Classification without documented criteria	Lowest
☆	No Assertion Provided	No classification submitted	None

What the Stars Mean

• 4 stars: Highest confidence - vetted by expert panels, used in clinical practice guidelines
• 3 stars: High confidence - expert panel review (e.g., ClinGen Variant Curation Expert Panel)
• 2 stars: Moderate confidence - consensus among multiple independent submitters
• 1 star: Single submitter with evidence - quality depends on submitter expertise
• 0 stars: Low confidence - insufficient evidence or no criteria provided

Conflicting Interpretations

What Constitutes a Conflict?

As of June 2022, conflicts are reported between:

• Pathogenic/likely pathogenic vs. Uncertain significance
• Pathogenic/likely pathogenic vs. Benign/likely benign
• Uncertain significance vs. Benign/likely benign

Conflict Resolution

When conflicts exist, ClinVar reports:

• "Conflicting interpretations of pathogenicity" - Disagreement on clinical significance
• Individual submissions are displayed so users can evaluate evidence
• Higher review status (more stars) carries more weight
• More recent submissions may reflect updated evidence

Handling Conflicts in Research

When encountering conflicts:

1. Check the review status (star rating) of each interpretation
2. Examine the evidence and criteria provided by each submitter
3. Consider the date of submission (more recent may reflect new data)
4. Review population frequency data and functional studies
5. Consult expert panel classifications when available

Aggregate Classifications

ClinVar calculates an aggregate classification when multiple submitters provide interpretations:

No Conflicts

When all submitters agree (within the same category):

• Display: Single classification term
• Confidence: Higher with more submitters

With Conflicts

When submitters disagree:

• Display: "Conflicting interpretations of pathogenicity"
• Details: All individual submissions shown
• Resolution: Users must evaluate evidence themselves

Interpretation Best Practices

For Researchers

1. Always check review status - Prefer variants with ★★★ or ★★★★ ratings
2. Review submission details - Examine evidence supporting classification
3. Consider publication date - Newer classifications may incorporate recent data
4. Check assertion criteria - Variants with ACMG criteria are more reliable
5. Verify in context - Population, ethnicity, and phenotype matter
6. Follow up on conflicts - Investigate discrepancies before making conclusions

For Variant Annotation Pipelines

1. Prioritize higher review status classifications
2. Flag conflicting interpretations for manual review
3. Track classification changes over time
4. Include population frequency data alongside ClinVar classifications
5. Document ClinVar version and access date

Red Flags

Be cautious with variants that have:

• Zero or one star rating
• Conflicting interpretations without resolution
• Classification as VUS (uncertain significance)
• Very old submission dates without updates
• Classification based on in silico predictions alone

Common Query Patterns

Search for High-Confidence Pathogenic Variants

BRCA1[gene] AND pathogenic[CLNSIG] AND practice guideline[RVSTAT]

Filter by Review Status

TP53[gene] AND (reviewed by expert panel[RVSTAT] OR practice guideline[RVSTAT])

Exclude Conflicting Interpretations

CFTR[gene] AND pathogenic[CLNSIG] NOT conflicting[RVSTAT]

Updates and Reclassifications

Why Classifications Change

Variants may be reclassified due to:

• New functional studies
• Additional population data (e.g., gnomAD)
• Updated ACMG guidelines
• Clinical evidence from more patients
• Segregation data from families

Tracking Changes

• ClinVar maintains submission history
• Version-controlled VCV/RCV accessions
• Monthly updates to classifications
• Reclassifications can go in either direction (upgrade or downgrade)

Key Resources

• ACMG/AMP Variant Interpretation Guidelines: Richards et al., 2015
• ClinGen Sequence Variant Interpretation Working Group: https://clinicalgenome.org/
• ClinVar Clinical Significance Documentation: https://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
• Review Status Documentation: https://www.ncbi.nlm.nih.gov/clinvar/docs/review_status/