VariantClassificationGateChecker

Variant Classification Gate

Liquid Biopsy жидкостная биопсия cfDNA ctDNA CTC exosomes NGS qPCR

Utility description: Variant Classification Gate

Variant Classification Gate Checker — Final Validation of Genetic Variant Classification

ℹ️ Utility performs independent audit of classification evidence base according to ACMG/AMP 2015 + SVI refinements, ClinGen VCEP, CAP/CLIA and EU IVDR:
• Criteria Sufficiency & Validity: Verification of criteria count and permissible combination (PVS1, PS1, PM2, etc.) for assigned class.
• Database Currency: Verification of ClinVar and gnomAD version currency against validated versions.
• ClinVar Conflict Detection: Identification of conflicting interpretations in public databases.
• Auto/Manual Concordance: Control of agreement between automated classification and expert review.
• Disease Context Match: Verification of classification applicability to patient's specific disease.
• Actionability Verification: Confirmation of therapeutic/diagnostic significance source.

⚠️ IMPORTANT:
• "Pathogenic" classification based solely on PM-criteria is INVALID per ACMG rules.
• Using outdated ClinVar version may miss variant reclassification.
• ClinVar conflict (>2 contradictory submissions) requires mandatory manual curation.
• Automated classification without manual review is unacceptable for clinical reports.

Usage:
VariantClassificationGateChecker.exe → demo mode (console output)
VariantClassificationGateChecker.exe input.csv output.json → evaluate your data

Input format:
SampleID,VariantID,Gene,Context,AssignedClassification,ClassificationFramework,AppliedCriteria,MinRequiredCriteria_Count,ActualCriteria_Count,CriteriaCombination_Valid,ClinVar_CurrentStatus,ClinVar_Conflict,ClinVar_SubmissionCount,DatabaseVersion_ClinVar,ValidatedDatabaseVersion_ClinVar,DatabaseVersion_GNomAD,ValidatedDatabaseVersion_GNomAD,ManualReview_Completed,ReviewerID,AutoManual_Concordant,DiseaseContext_Matched,IsActionable,ActionabilityVerified

Example:
NGS-001,BRCA1:c.5266dupC,BRCA1,Germline,Pathogenic,ACMG_AMP_2015,PVS1+PS1+PM2,2,3,true,Pathogenic,false,45,2026-05,2026-05,v4.1,v4.1,true,DR-SMITH,true,true,true,true

📍 Scope of Application (Usage Where):
• Clinical Laboratories: Final gate before variant inclusion in report.
• Molecular Tumor Boards: Objective basis for complex variant discussion.
• Bioinformatics Pipeline Validation: Confirmation of correct ACMG rules implementation.
• Regulatory Inspections: Demonstration of classification quality control system.

— WHY IS THIS NEEDED?
Variant classification determines patient fate: surgery, therapy, family screening.
Classification errors are the most frequent cause of litigation in molecular diagnostics.
Independent evidence base audit eliminates systematic rule engine errors and stale data.
This is the last barrier between raw data and clinical decision.

⚠️ CRITICAL:
• Criteria Combination Valid: Invalid combination = INVALID. Classification has no standing.
• DB Versions Current: Outdated databases = risk of using reclassified variants.
• ClinVar Conflict: Requires manual curation. Automated decision unacceptable.
• Auto/Manual Concordance: Discordance = CONFLICT. Third expert review required.
• Manual Review: Mandatory for Pathogenic/LP/Tier I-II. Absence = NEEDS_REVIEW.
• Disease Context: Classification outside context = potential error (e.g., CFTR in oncology).

Key features:
• Seven-parameter evidence base audit
• Detection of invalid ACMG/AMP criteria combinations
• Integration with external database versions
• Four-tier classification (Validated / Needs Review / Conflict / Invalid)
• Compliance with ACMG/AMP + SVI + ClinGen + CAP/CLIA

Critical parameters:
• Criteria Combination: Valid per ACMG/SVI rules
• Criteria Count: ≥ Minimum required
• ClinVar Version: = Validated version
• gnomAD Version: = Validated version
• ClinVar Conflict: False
• Auto/Manual Concordance: True
• Manual Review: Completed (for clinical-grade)
• Disease Context: Matched
• Actionability: Verified (if actionable)

💡 Usage tips:
1. SVI Refinements: Use current ClinGen SVI recommendations, not only original 2015 rules.
2. VCEP Specifications: For genes with ClinGen VCEP, use gene-specific criteria instead of generic ACMG.
3. DB Update Cycle: Synchronize database updates with pipeline validation cycle.
4. Conflict Resolution Protocol: Pre-define conflict resolution procedure (third expert, functional data).
5. Audit Trail: Retain complete criteria set and database versions for every classified variant.

⚠️ Note: This utility verifies CLASSIFICATION EVIDENCE BASE, not its clinical truth. Truth is determined by totality of scientific data and expert judgment. The utility guarantees that classification is justified, reproducible, and compliant with approved standards.

input.csv

SampleID,VariantID,Gene,Context,AssignedClassification,ClassificationFramework,AppliedCriteria,MinRequiredCriteria_Count,ActualCriteria_Count,CriteriaCombination_Valid,ClinVar_CurrentStatus,ClinVar_Conflict,ClinVar_SubmissionCount,DatabaseVersion_ClinVar,ValidatedDatabaseVersion_ClinVar,DatabaseVersion_GNomAD,ValidatedDatabaseVersion_GNomAD,ManualReview_Completed,ReviewerID,AutoManual_Concordant,DiseaseContext_Matched,IsActionable,ActionabilityVerified
NGS-2026-001,BRCA1:c.5266dupC,BRCA1,Germline,Pathogenic,ACMG_AMP_2015,PVS1+PS1+PM2,2,3,true,Pathogenic,false,45,2026-05,2026-05,v4.1,v4.1,true,DR-SMITH,true,true,true,true
NGS-2026-001,CHEK2:c.1100delC,CHEK2,Germline,Likely Pathogenic,ACMG_AMP_2015,PVS1+PM2,2,2,true,Conflicting interpretations,true,18,2026-05,2026-05,v4.1,v4.1,true,DR-JONES,false,true,false,true
NGS-2026-002,TP53:c.743G>A,TP53,Somatic,Tier I,AMP_ASCO_CAP_2017,Level_A,1,1,true,Pathogenic,false,12,2025-11,2026-05,v4.0,v4.1,false,,true,true,true,true
NGS-2026-003,MYH7:c.1208T>C,MYH7,Germline,Pathogenic,ACMG_AMP_2015,PM1+PM2+PP3,2,3,false,VUS,false,5,2026-05,2026-05,v4.1,v4.1,true,DR-LEE,false,false,false,true

URS & FS — User Requirements and Functional Specification

This document describes the controlled interface and behaviour of VariantClassificationGateChecker for Variant Classification Gate Checker.

Domain limits URS input.csv FS IQ/OQ/PQ

Domain limits and critical parameters

Key fragments from the source description are shown below. Before production use, limits must be verified against the approved specification, registration dossier and local SOPs.

• ClinVar conflict (>2 contradictory submissions) requires mandatory manual curation.
⚠️ CRITICAL:
Critical parameters:
• Criteria Count: ≥ Minimum required

URS — User Requirements Specification

ID	Requirement	Criticality	Acceptance criterion
URS-001	The utility shall accept an input.csv file for Variant Classification Gate Checker with headers defined in the data contract.	High	The file is processed without manual header editing.
URS-002	The utility shall perform deterministic QC evaluation without machine learning and without probabilistic conformance decisions.	High	Identical input data, rule version and configuration produce reproducible results.
URS-003	The utility shall validate mandatory fields, data types, ranges, units and domain plausibility.	High	Schema, conversion and range errors are explicitly reported.
URS-004	The utility shall apply domain limits and rules from the description, approved specification, registration dossier and local SOPs.	High	Each check has PASS/WARNING/FAIL and a clear message.
URS-005	The utility shall generate output.json with machine-readable results, source values, warnings, failures and critical findings.	High	JSON is suitable for LIMS/ELN/MES integration and QA/QC review.
URS-006	The utility shall preserve traceability between batch/sample, input file, applied rules and final status.	High	Output contains identifiers, checked parameters and audit metadata.
URS-007	The documentation shall support IQ/OQ/PQ, CSV/CSA and review by internal QA or inspectors.	Medium	URS, FS, input/output contract and test scenarios are supplied with the utility.
URS-008	The utility shall be used as a QC decision-support tool and not as a substitute for approved specifications and QA/QP release decision.	Medium	Documentation states change control and limit-verification expectations.

input.csv contract

#	Field	Type	Sample	Purpose
1	`SampleID`	string / controlled vocabulary	`NGS-2026-001`	Sample or laboratory specimen identifier.
2	`VariantID`	string / controlled vocabulary	`BRCA1:c.5266dupC`	Controlled input parameter for deterministic QC rules.
3	`Gene`	string / controlled vocabulary	`BRCA1`	Controlled input parameter for deterministic QC rules.
4	`Context`	string / controlled vocabulary	`Germline`	Controlled input parameter for deterministic QC rules.
5	`AssignedClassification`	string / controlled vocabulary	`Pathogenic`	Controlled input parameter for deterministic QC rules.
6	`ClassificationFramework`	string / controlled vocabulary	`ACMG_AMP_2015`	Controlled input parameter for deterministic QC rules.
7	`AppliedCriteria`	string / controlled vocabulary	`PVS1+PS1+PM2`	Controlled input parameter for deterministic QC rules.
8	`MinRequiredCriteria_Count`	integer / decimal	`2`	Count parameter used for microbiological, particulate or cellular control.
9	`ActualCriteria_Count`	integer / decimal	`3`	Count parameter used for microbiological, particulate or cellular control.
10	`CriteriaCombination_Valid`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
11	`ClinVar_CurrentStatus`	string / controlled vocabulary	`Pathogenic`	Result/status used in final classification.
12	`ClinVar_Conflict`	string / controlled vocabulary	`false`	Controlled input parameter for deterministic QC rules.
13	`ClinVar_SubmissionCount`	integer / decimal	`45`	Count parameter used for microbiological, particulate or cellular control.
14	`DatabaseVersion_ClinVar`	string / controlled vocabulary	`2026-05`	Controlled input parameter for deterministic QC rules.
15	`ValidatedDatabaseVersion_ClinVar`	string / controlled vocabulary	`2026-05`	Controlled input parameter for deterministic QC rules.
16	`DatabaseVersion_GNomAD`	string / controlled vocabulary	`v4.1`	Controlled input parameter for deterministic QC rules.
17	`ValidatedDatabaseVersion_GNomAD`	string / controlled vocabulary	`v4.1`	Controlled input parameter for deterministic QC rules.
18	`ManualReview_Completed`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
19	`ReviewerID`	string / controlled vocabulary	`DR-SMITH`	Controlled input parameter for deterministic QC rules.
20	`AutoManual_Concordant`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
21	`DiseaseContext_Matched`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
22	`IsActionable`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
23	`ActionabilityVerified`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.

SampleID,VariantID,Gene,Context,AssignedClassification,ClassificationFramework,AppliedCriteria,MinRequiredCriteria_Count,ActualCriteria_Count,CriteriaCombination_Valid,ClinVar_CurrentStatus,ClinVar_Conflict,ClinVar_SubmissionCount,DatabaseVersion_ClinVar,ValidatedDatabaseVersion_ClinVar,DatabaseVersion_GNomAD,ValidatedDatabaseVersion_GNomAD,ManualReview_Completed,ReviewerID,AutoManual_Concordant,DiseaseContext_Matched,IsActionable,ActionabilityVerified
NGS-2026-001,BRCA1:c.5266dupC,BRCA1,Germline,Pathogenic,ACMG_AMP_2015,PVS1+PS1+PM2,2,3,true,Pathogenic,false,45,2026-05,2026-05,v4.1,v4.1,true,DR-SMITH,true,true,true,true
NGS-2026-001,CHEK2:c.1100delC,CHEK2,Germline,Likely Pathogenic,ACMG_AMP_2015,PVS1+PM2,2,2,true,Conflicting interpretations,true,18,2026-05,2026-05,v4.1,v4.1,true,DR-JONES,false,true,false,true
NGS-2026-002,TP53:c.743G>A,TP53,Somatic,Tier I,AMP_ASCO_CAP_2017,Level_A,1,1,true,Pathogenic,false,12,2025-11,2026-05,v4.0,v4.1,false,,true,true,true,true

Input validation rules

ID	Field	Rule	Criticality
VR-001	`SampleID`	The field shall match an approved dictionary or accepted string representation.	High
VR-002	`VariantID`	The field shall match an approved dictionary or accepted string representation.	High
VR-003	`Gene`	The field shall match an approved dictionary or accepted string representation.	High
VR-004	`Context`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-005	`AssignedClassification`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-006	`ClassificationFramework`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-007	`AppliedCriteria`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-008	`MinRequiredCriteria_Count`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-009	`ActualCriteria_Count`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-010	`CriteriaCombination_Valid`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-011	`ClinVar_CurrentStatus`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-012	`ClinVar_Conflict`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-013	`ClinVar_SubmissionCount`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-014	`DatabaseVersion_ClinVar`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-015	`ValidatedDatabaseVersion_ClinVar`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-016	`DatabaseVersion_GNomAD`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-017	`ValidatedDatabaseVersion_GNomAD`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-018	`ManualReview_Completed`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-019	`ReviewerID`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-020	`AutoManual_Concordant`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-021	`DiseaseContext_Matched`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-022	`IsActionable`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-023	`ActionabilityVerified`	The field shall match an approved dictionary or accepted string representation.	Medium

FS — Functional Specification

ID	Function	Implementation
FS-001	CLI execution	Support execution modes: demo mode without arguments and production mode input.csv output.json.
FS-002	CSV import	Read input.csv in UTF-8/CSV-compatible format and validate header and expected columns.
FS-003	Schema validation	Check mandatory fields, column count, unknown key fields and empty mandatory values.
FS-004	Type conversion	Convert numeric, flag and text values; invalid format is recorded as a row-level error.
FS-005	Domain rule engine	Apply rules for Variant Classification Gate Checker, including critical limits from the description and approved specification.
FS-006	Status aggregation	Produce final status: FAIL for critical failure, WARNING for non-critical deviation, PASS for conformance.
FS-007	JSON export	Write output.json with detailed checks, source values, warnings, failures and critical findings.
FS-008	Audit support	Keep result structure suitable for review, deviation investigation and calculation reproduction.
FS-009	Integration contract	Support the scenario LIMS/ELN/MES → input.csv → utility → output.json → portal/admin review.
FS-010	Error handling	Return explicit messages for missing file, empty CSV, invalid schema, output write failure and invalid format.

Example output.json

{
  "utilityId": "variantclassificationgatechecker",
  "utilityFolder": "VariantClassificationGateChecker",
  "package": "LiquidBiopsy",
  "overallStatus": "PASS|WARNING|FAIL",
  "sourceFile": "input.csv",
  "processedAtUtc": "2026-06-10T00:00:00Z",
  "checks": [
    {
      "parameter": "SampleID",
      "value": "NGS-2026-001",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-001"
    },
    {
      "parameter": "VariantID",
      "value": "BRCA1:c.5266dupC",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-002"
    },
    {
      "parameter": "Gene",
      "value": "BRCA1",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-003"
    },
    {
      "parameter": "Context",
      "value": "Germline",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-004"
    },
    {
      "parameter": "AssignedClassification",
      "value": "Pathogenic",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-005"
    },
    {
      "parameter": "ClassificationFramework",
      "value": "ACMG_AMP_2015",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-006"
    },
    {
      "parameter": "AppliedCriteria",
      "value": "PVS1+PS1+PM2",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-007"
    },
    {
      "parameter": "MinRequiredCriteria_Count",
      "value": "2",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-008"
    },
    {
      "parameter": "ActualCriteria_Count",
      "value": "3",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-009"
    },
    {
      "parameter": "CriteriaCombination_Valid",
      "value": "true",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-010"
    },
    {
      "parameter": "ClinVar_CurrentStatus",
      "value": "Pathogenic",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-011"
    },
    {
      "parameter": "ClinVar_Conflict",
      "value": "false",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-012"
    }
  ],
  "criticalFindings": [],
  "warnings": [],
  "audit": {
    "inputHash": "sha256:<calculated at runtime>",
    "rulesVersion": "<utility executable version>",
    "documentation": "VariantClassificationGateChecker.documentation.html"
  }
}

Traceability matrix

URS	FS	Test	Evidence
URS-001	FS-001, FS-002	OQ-001	Verify execution and import of valid input.csv.
URS-002	FS-005, FS-006	OQ-004	Repeat the same dataset and compare output.json.
URS-003	FS-003, FS-004, FS-010	OQ-002, OQ-003	Verify missing columns and invalid types.
URS-004	FS-005, FS-006	OQ-004, PQ-001	Verify critical deviations on real/boundary data.
URS-005	FS-007, FS-009	OQ-005	Verify JSON schema and downstream-system suitability.
URS-006	FS-008	OQ-006	Verify identifiers and audit metadata.
URS-007	FS-008, FS-010	IQ-001, OQ-007	Verify documentation completeness and control evidence.
URS-008	FS-005, FS-008	PQ-002	Verify review workflow and no replacement of QA decision.

IQ/OQ/PQ test scenarios

ID	Scenario	Expected result
IQ-001	Verify executable, input.csv, documentation and checksum availability.	Delivery set is complete; version is recorded.
OQ-001	Valid sample row from input.csv.	PASS or acceptable WARNING according to rules.
OQ-002	Remove a mandatory CSV column.	Schema error or FAIL with missing-column reference.
OQ-003	Place a non-numeric value into a numeric field.	Type-conversion error with row/field reference.
OQ-004	Set a critical parameter outside the limit.	FAIL and critical finding.
OQ-005	Verify output.json structure.	All mandatory sections are present and JSON is valid.
OQ-006	Verify batch/sample traceability.	Input and result identifiers match.
PQ-001	Verify 3–5 real user batches/samples.	Result is confirmed by QC/QA review.
PQ-002	Verify deviation workflow and manual QA decision.	Utility supports review but does not replace approved decision.

QA/QC and change control

Do not rename columns without updating validator, documentation and test set.
Retain input.csv, output.json, executable version and checksum.
Before production use, perform IQ/OQ/PQ or equivalent CSV/CSA verification.
Critical limits shall be verified against the approved specification, registration dossier and local SOPs.
The utility provides structured QC decision support; final release decision remains with QA/QP and approved procedures.

Included in packages

Liquid Biopsy QC Suite

QC and pre-analytical control package for liquid biopsy workflows: cfDNA/ctDNA, CTC, EV/exosomes, methylation, NGS/qPCR/ddPCR, sample quality, contamination, sensitivity and reporting checks.

Open