SNVs and indels
Variants annotated with the MANE transcript, population frequencies, calibrated predictors such as REVEL, AlphaMissense and SpliceAI, and ClinVar classifications.
NeoGenomica software
NeoVar: the analysis behind every report.
A platform developed by NeoGenomica to analyse the variants found in exomes, genomes and panels. It brings together the evidence for each variant, shows the classification criterion by criterion and records the review by a second professional before the report.
- Origin
- Developed by NeoGenomica
- Classification
- Visible reasoning for every criterion
- Population
- Brazilian frequencies in the rules
- After your results
- Infinity VUS and Infinity Genes
Scope of the analysis
Every class of variant in one place.
The analyst reviews sequence, structure and hard-to-read regions within the same case, without switching between systems.
CNVs and structural variants
Calls from different algorithms, ClinGen dosage, exon-level evidence and ACMG/ClinGen classification for CNVs. In the hybrid genome, long reads are shown during review.
Mitochondrial DNA and pseudogenes
Heteroplasmy and mitochondrial-specific databases, plus a dedicated workflow for genes with segmental duplications, such as PMS2.
The classes of variant assessed in each case depend on the test ordered and the sequencing technology.
Analysis workflow
From the sequencing file to the report.
Every case follows the same steps, with the team decisions on record.
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01
Case intake
Sample, test, panel and clinical data arrive from the laboratory system, with no retyping.
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02
Versioned annotation
Each variant receives frequencies, predictions and clinical evidence, with the version of every database recorded.
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03
Analysis and classification
The analyst filters, prioritises and classifies the variants following ACMG/AMP and ClinGen guidelines.
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04
Two-person review
A second professional reviews the selected variants before they are sent to the report.
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05
Report and follow-up
The report is issued in NeoReport, and reported VUS are then followed by Infinity VUS.
ACMG classification
A classification that shows its reasoning.
NeoVar does not deliver just a class. It shows which evidence supports the suggestion, where it came from and what is still missing.
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One scenario per disease
The same variant is assessed separately for each disease, mode of inheritance and mechanism associated with the gene.
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Criterion by criterion
All 28 ACMG/AMP criteria are shown with the source consulted, including when the available evidence is still insufficient.
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Expert rules
When a ClinGen expert panel has published its own rules for the gene, those rules are applied.
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Specialist decision
The final classification is always made by a specialist. Evidence gathered by automated tools, including artificial intelligence, only counts once it has been verified.
ACMG/AMP classification
Fictitious variant
Scenario assessed
Autosomal dominant disease caused by loss of function
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PVS1Loss-of-function variant in a gene with this mechanism Met -
PM2Absent or very rare in gnomAD and ABraOM Met at supporting level -
PS3Published functional studies Insufficient evidence -
BS1Frequency higher than expected for the disease Not met
Suggestion: likely pathogenic, for specialist review
Population data
Built for the Brazilian population.
International databases do not always represent the genetic diversity of Brazil. NeoVar adds Brazilian data to them.
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Brazilian frequencies
Besides gnomAD, the frequency rules take into account ABraOM, a database of variants in the Brazilian population.
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Internal cohort
The frequency of each variant and each CNV across tests already analysed by NeoGenomica helps to recognise recurrent findings and possible technical artefacts.
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Phenotype in Portuguese
The clinical signs described in the test request are converted into HPO terms and checked against the official ontology before they guide the analysis.
Two-person review
A second person in every decision.
The NeoVar workflow separates who analyses from who finalises. By default, whoever analysed a case cannot finalise it alone.
- 01
Independent analysis
When two analysts work on the same case, each one’s choices stay hidden from the other until they finish.
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Consolidated review
The selections are compared variant by variant, and the agreement between analysts is recorded.
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Finalised by another professional
Sending the case to the report requires a professional other than the one who did the analysis.
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Report release
In NeoReport, the report is reviewed and released manually by a responsible specialist.
Technical performance
Measured against a public reference.
These metrics assess the bioinformatics pipeline that feeds NeoVar, compared with the Genome in a Bottle (GIAB) reference for the HG002 sample. They show what long reads add to the detection of structural variants.
- Structural variants detected (sensitivity)
- Short-read21%
- Hybrid, about 10×67%
- Hybrid, 20×74%
- Calls confirmed by the reference (precision)
- Short-read78%
- Hybrid, about 10×86%
- Hybrid, 20×86%
- Sensitivity in challenging medically relevant genes (CMRG)
- Short-read29%
- Hybrid, about 10×66%
- Hybrid, 20×76%
| Metric | Short-read genome | Hybrid with about 10× long-read coverage | Hybrid with 20× long-read coverage |
|---|---|---|---|
| Structural variants detected (sensitivity) | 21% | 67% | 74% |
| Calls confirmed by the reference (precision) | 78% | 86% | 86% |
| Sensitivity in challenging medically relevant genes (CMRG) | 29% | 66% | 76% |
Internal assessment on a single reference sample (HG002), carried out in May 2026, not peer reviewed. GIAB v5.0q reference with 28,145 structural variants of 50 base pairs or more, compared with Truvari v5.4 using only calls that passed the filters. CMRG: 216 structural variants in clinically relevant genes that are hard to sequence. All configurations use about 30× short-read coverage; long reads are PacBio HiFi. Performance for each patient depends on the sample, the coverage and the region analysed.
NeoReport
From NeoVar to the report, with no retyping.
The classification made in NeoVar reaches NeoReport as structured data. The report is written, reviewed and released by a specialist.
- Findings organised as primary, secondary and carrier
- A Bayesian scale that places each VUS between benign and pathogenic
- Preserved versions and formal correction when needed
- Digitally signed with an ICP-Brasil certificate
Real excerpt from the NeoReport demonstration environment, cut without personal data.
Follow-up after the report
The test ends with the report. The investigation does not.
In NeoGenoma and NeoExoma, Infinity Genes reanalyzes negative exomes and genomes every month and cross-checks each new OMIM gene-disease association incorporated by the team against the stored rare variants, with no new sample collection and no extra cost. Findings confirmed by the team are communicated to the requesting physician.
All NeoGenomica tests include Infinity VUS to follow reported variants of uncertain significance. When a relevant reclassification is confirmed after specialist review, the doctor is notified and the report may be updated.
See how the follow-up worksFrequently asked questions
About NeoVar.
Does artificial intelligence make the diagnosis?
No. Automated features organise evidence and suggest priorities for review. Variant classification, the case conclusion and the release of the report are done by specialists.
Which tests go through NeoVar?
Exomes, genomes and sequencing panels performed by NeoGenomica, including somatic oncology panels, are analysed in NeoVar according to the workflow of each test.
How can I tell what evidence a variant was classified with?
Each case records the versions of the databases consulted, such as ClinVar, OMIM, ClinGen, HPO and PanelApp. This way, the classification can be reviewed in light of the evidence available on the date of the analysis.
Do the solved cases identify patients?
No. The solved cases page only shows the gene, the variant and, when available, HPO terms, with no name, age, sex, test number or other identifiers.
Can NeoVar be used in research projects?
Yes. Research projects can include variant analysis and prioritisation with NeoVar, according to the approved scope.
Explore the research servicesNext step
Discuss a case with the team.
Talk to our specialists about the testing strategy and the analysis of your patient’s variants.
