Analysis Workflow
Variant Analysis & Classification
From VCF to a fully classified variant set with complete evidence attribution. Helena annotates every variant through Ensembl VEP and applies the 2015 ACMG/AMP guidelines as deterministic, rule-based logic, never as AI prediction.
All 28 evidence criteria are evaluated systematically against population data, clinical archives, computational predictions, and gene-level constraint metrics. Every applied criterion is documented and traceable.
Core Capabilities
Four pillars of clinical-grade variant interpretation built into a single, integrated workflow.
VCF Processing
Standard VCF 4.1 and 4.2 parsing from any sequencing platform. Whole genome, whole exome, and targeted panels supported. Quality filtering preserves clinically significant ClinVar variants regardless of quality scores.
Comprehensive Annotation
Ensembl VEP for consequence prediction, protein impact, and functional domain mapping. Multi-source enrichment from ClinVar, gnomAD, dbNSFP, ClinGen, and 12+ in silico predictors. Over 60 annotations per variant.
Rule-Based ACMG/AMP Classification
All 28 evidence criteria from the 2015 ACMG/AMP guidelines (Richards et al.) systematically evaluated. No AI determines pathogenicity. Five-tier output: Pathogenic, Likely Pathogenic, VUS, Likely Benign, Benign.
Complete Audit Trail
Every applied criterion is explicitly documented per variant. Classification rationale is fully traceable to evidence sources. Reproducible results across runs for the same input.
Technical Foundation
Helena integrates authoritative genomic and clinical resources into the classification pipeline. Every variant is evaluated against this combined evidence base.
Ensembl VEP
Variant effect prediction, consequence, protein impact
ClinVar
Clinical variant interpretations and review status
gnomAD
Population allele frequencies (global and population-specific)
ClinGen
Gene-disease validity and dosage sensitivity
dbNSFP
Aggregated functional predictions across 12+ tools
AlphaMissense
Missense pathogenicity prediction (DeepMind)
SpliceAI
Splice site impact prediction
BayesDel
Meta-predictor with ClinGen SVI-calibrated thresholds
GERP++ / PhyloP / PhastCons
Evolutionary conservation
pLI / LOEUF / o/e
Gene-level constraint metrics
ACMG/AMP Criteria Coverage
All 28 evidence criteria from the 2015 ACMG/AMP guidelines are systematically evaluated. Pathogenic and benign evidence is weighted according to standard combining rules.
PVS1
Very Strong Pathogenic
- PVS1, Null variant in gene with established LOF mechanism
PS1–PS4
Strong Pathogenic
- PS1, Same amino acid change as established pathogenic
- PS2, De novo (paternity and maternity confirmed)
- PS3, Functional studies showing damaging effect
- PS4, Significantly increased prevalence in affected individuals
PM1–PM6
Moderate Pathogenic
- PM1, Mutational hot spot or critical functional domain
- PM2, Absent or extremely low frequency in population databases
- PM3, Detected in trans with a pathogenic variant (recessive)
- PM4, Protein length changes (in-frame indels, stop-loss)
- PM5, Novel missense at residue with different pathogenic change
- PM6, Assumed de novo without confirmation of paternity/maternity
PP1–PP5
Supporting Pathogenic
- PP1, Cosegregation with disease in multiple affected family members
- PP2, Missense in gene with low rate of benign missense variants
- PP3, Multiple computational lines of evidence support deleterious effect
- PP4, Patient phenotype highly specific for the gene
- PP5, Reputable source reports as pathogenic
BA1
Stand-alone Benign
- BA1, Allele frequency above 5% in population databases
BS1–BS4
Strong Benign
- BS1, Allele frequency greater than expected for disease
- BS2, Observed in healthy adults (recessive, dominant, X-linked)
- BS3, Functional studies showing no damaging effect
- BS4, Lack of segregation in affected family members
BP1–BP7
Supporting Benign
- BP1, Missense in gene where only truncating cause disease
- BP2, Observed in trans with pathogenic (dominant) or in cis
- BP3, In-frame indel in repetitive region without known function
- BP4, Multiple computational lines of evidence suggest no impact
- BP5, Variant found in case with alternate molecular basis
- BP6, Reputable source reports as benign
- BP7, Synonymous with no predicted splice impact and conserved
What You Receive
The output of this workflow is a fully classified, fully documented variant set ready for clinical review and downstream phenotype matching.
Classified Variant Table
Every variant in the input VCF receives a five-tier ACMG classification with explicit listing of all applied criteria.
Evidence Detail Per Variant
Population frequencies, ClinVar status, in silico predictions, conservation scores, and gene constraint metrics in one unified view.
Criteria Audit Trail
For each criterion applied (e.g., PVS1, PM2_supporting), the underlying evidence and threshold used is documented and traceable.
Confidence Scoring
Numerical confidence score per classification reflects the strength and number of supporting criteria, helping prioritize review.
See Variant Classification in Practice
Request a demo to see how Helena classifies a real VCF, from raw upload to a fully evidenced variant table ready for clinical review.