Platform / Databases / Atlas
Atlas
Helena Bioinformatics' own database of classified genetic variants.
Atlas brings together variant annotations, scientific evidence and classifications produced by Helena. It turns the work of analysing individual variants into a reusable resource for Folklore and genomic research.
What Helena builds
Atlas grows from variants processed by Helena and candidates drawn from scientific resources such as ClinVar, dbNSFP, AlphaMissense, SpliceAI, gnomAD, Geno2MP, VKGL and ClinGen ERepo. Helena normalises their identities, removes duplicates, gathers annotations and applies its own classification pipeline under the ACMG framework.
The resulting records combine evidence with Helena's classifications and the criteria behind them. Helena's contribution is the integrated, reproducible analysis and the database that makes this work reusable.
Inside Atlas
121,847,846 unique classified variants
Nuclear single-nucleotide variants and small insertions and deletions, on GRCh38.
| ACMG class | Variants |
|---|---|
| Pathogenic | 199,636 |
| Likely pathogenic | 1,290,399 |
| Uncertain significance | 103,994,556 |
| Likely benign | 7,139,944 |
| Benign | 9,223,311 |
Statistics checked . Each record represents a unique variant.
The five classes include uncertain significance, where the available evidence does not support a pathogenic or benign conclusion. These are automated classifications, not individual clinical validations of every record.
A record in Atlas
This real record shows how a variant identity, annotation and supporting evidence sit alongside Helena's classification.
| Variant | chr1:121275026 C>T (GRCh38) |
|---|---|
| Gene and consequence | SRGAP2C; intronic variant |
| Atlas classification | Benign |
| Recorded ACMG criteria | BA1, BS2 |
| Population evidence | Allele frequency 5.95%; 8,958 of 150,636 alleles; 476 homozygous observations |
Population observations are stored alongside the classification, allowing the supporting evidence to be reviewed and reused.
Selected fields from the stored Atlas record, checked 27 September 2026. The public Folklore analysis can use a newer methodology and report updated criteria.
View the population evidence in gnomADWhy Atlas matters
The same genetic variant can appear in many different analyses. Atlas allows Folklore to reuse its existing annotations and evidence when they are compatible with the current analysis, reducing repeated processing and providing a consistent basis for interpretation.
For research collaborations, the same resource can support variant annotation and comparison across cohorts. The scientific question, data access and analysis are defined for each project.
Quality, traceability and updates
Each database release is tied to a defined methodology and reference-data configuration. Checks cover unique variant identities, required annotations, supported classifications and consistency across the release. A replacement is validated before publication.
Folklore checks compatibility before reusing a record. Variants without a compatible match follow the normal analysis workflow. The patient's symptoms, genotype and family information are assessed separately for the case.
Atlas contains no patient identities, sample genotypes or case histories. Its scope covers nuclear single-nucleotide variants and small insertions and deletions; structural and mitochondrial variants have separate Folklore workflows.
Read the classification methodology