01 · CASE INTAKE
Accept the data clinicians actually receive.
Support for VCF and BAM/CRAM workflows, with paired-end Illumina FASTQ support for the validated GRCh38 path.
See workflow →Clinical genomics decision support
From genomic data to reviewable clinical evidence.
LYNNAGEN brings variant interpretation, phenotype context, technical quality, and evidence provenance into one clinician-led review workspace.
Five-tier pathogenicity
Auditable provenance
Professional review remains final
Clinical Genomics Workspaceprofessional decision support
From sequence data to reviewable clinical evidence
Clinical evidence, technical QC and patient relevance remain distinct.
01 · INTAKECase and sequence input
02 · PROCESSAlignment and normalization
03 · INTERPRETEvidence and classification
04 · REVIEWClinician / laboratory decision
Start a genomic case
FASTQ R1/R2, BAM, CRAM or VCF
Evidence coverage
ClassificationClinVar / ClinGenReady
Gene / diseaseGenCC / ClinGenReady
PhenotypeHPO / MONDOReady
AnnotationVEP / MANEReady
PopulationgnomADQuery + cache
FunctionalMaveDB / AlphaMissenseReady
Pathogenicity remains primaryFive-tier interpretation stays visible and scannable.
Patient relevance stays distinctPhenotype and disease context do not silently overwrite pathogenicity.
Technical QC stays separateQuality signals remain reviewable rather than hidden in the classification.
Provenance remains visibleEvidence source, context, and limitations are kept auditable.
Platform
Built around the clinical review task.
LYNNAGEN organizes genomic analysis into a durable review workflow instead of collapsing every signal into a single opaque answer.
02 · VARIANT REVIEW
Keep the five-tier interpretation easy to scan.
Pathogenic, likely pathogenic, VUS, likely benign, and benign remain the primary classification dimension.
See review model →03 · EVIDENCE DOSSIER
Show where each conclusion comes from.
Variant identity, disease context, phenotype relevance, technical QC, and source evidence remain inspectable.
Explore evidence →Clinical workflow
One review path from intake to decision.
The product is organized around four explicit stages so the reviewer can see what happened to the case and where each evidence layer belongs.
01
Intake
Bring the case and patient context into a controlled workspace.
- VCF / BAM / CRAM / FASTQ
- Assembly selection
- Phenotype and HPO context
02
Process
Normalize and validate the data before evidence matching.
- Reference-aware normalization
- Alignment / calling where applicable
- Technical quality review
03
Interpret
Aggregate installed evidence without erasing source distinctions.
- Five-tier pathogenicity
- Gene–disease context
- Phenotype relevance
04
Review
Put the evidence dossier in front of the qualified reviewer.
- Provenance and conflicts
- Reviewer rationale
- Clinician / laboratory decision
Review model
Separate the questions that should stay separate.
A pathogenic variant is not automatically a patient diagnosis. LYNNAGEN keeps intrinsic variant assessment, patient-specific relevance, and technical validity visible as different review dimensions.
Variant pathogenicity
Five-tier classification remains the primary headline rather than being replaced by phenotype or QC signals.
Patient relevance
Phenotype and disease-context evidence help prioritize relevance to the patient without silently changing intrinsic pathogenicity.
Technical QC
Sequence and call-quality information remains an independent review lane.
Interpretation workspace
Structured evidence. Explicit review.
Illustrative review model — not a patient result.
Primary five-tier classification
Pathogenic
Likely
pathogenic
pathogenic
VUS
Likely
benign
benign
Benign
Patient relevancePhenotype / disease fit
Technical QCCall and sequence quality
ProvenanceSource / context / version
Qualified clinician or laboratory reviewer remains the final decision-maker.
Evidence & provenance
Evidence organized by purpose, not flattened into one score.
LYNNAGEN can surface classification, gene–disease, phenotype, population, transcript, annotation, and functional evidence while preserving source identity and review context.
Public assertions stay attributable.
Variant-level assertions are presented with their source context rather than silently becoming a new machine assertion.
Interpret variants in disease context.
Gene–disease validity, inheritance, and disease relationships remain available alongside variant evidence.
Connect patient presentation without rewriting pathogenicity.
Phenotype context helps prioritize diseases and patient relevance as a separate dimension.
Bring frequency and transcript context into review.
Population queries and local annotation resources support evidence review while retaining assembly and transcript context.
Deployment & governance
Designed for controlled clinical environments.
The public website and the clinical application should remain separate systems. Patient and genomic data should not pass through the marketing site.
Local-first data architecture
Large evidence, reference, runtime, and case assets can remain inside the controlled deployment environment.
Reference-aware matching
Unsafe identity or reference mismatches should remain visible rather than being forced into a clinical classification.
Durable case records
Case continuity and audit records persist across application and WSL restarts.
Professional governance
Final clinical interpretation remains with the qualified clinician or laboratory reviewer.
Request a demo
See LYNNAGEN in a clinical review workflow.
For clinical genetics, molecular diagnostics, pathology, and diagnostic laboratory teams evaluating structured genomic interpretation workflows.