From sequencing data to
annotated insight.
Guided variant detection and gene-level annotation built on curated clinical databases. Upload your VCF file or load a pre-configured sample to begin.
Upload Sequencing Data
Select a standard Variant Call Format (.vcf) file to begin.
The pipeline, in four steps
- Parse the uploaded VCF for a variant's position (or rsID).
- Query Ensembl VEP, which aggregates dbSNP, ClinVar, and gnomAD annotations for that exact variant.
- Fetch the gene's real exon structure and chromosome location from Ensembl.
- Ask an LLM to write a plain-language summary, constrained to only the facts retrieved above — it's told explicitly to say "not found" rather than invent anything.
Known limitations
- Assumes the GRCh38 genome build; flags a warning if a file specifies otherwise.
- Annotates one variant at a time (a picker appears for multi-variant files).
- OMIM is not yet connected — it requires a registered API key.
- The curated library below is illustrative/educational, not a diagnostic reference.
Click to browse or drag VCF file here
No VCF on hand? Run a curated clinical variant:
| Aspect | BaseRead | VarSome | Franklin |
|---|---|---|---|
| Cost | Free, open-source demo | Free tier + paid API | Free for clinical use |
| Narrative summary | LLM-generated, source-cited | Rule-based annotation | Curated clinical text |
| Transparency | Shows raw API response + sources | Partial (report view) | Partial (report view) |
| Clinical validation | None — educational prototype | Widely used in practice | Widely used in practice |
| Best for | Learning & demonstration | Clinical variant curation | Clinical genetic testing labs |
BaseRead is a student-built educational prototype, not a validated clinical tool — this comparison is about approach, not accuracy.
Curated Variant Library
Search or browse by category, then run the full annotation pipeline on any entry.
Live Validation Dashboard
Queries Ensembl live for each curated variant's real ClinVar significance and consequence, and checks it against what BaseRead's library expects — a live accuracy check, not a hand-picked demo.
| Gene | Variant | Live check | Live consequence |
|---|
Multiple variants found
Pick one to annotate.
GENE
Input: file.vcf · 0 variants
Gene Structure & Variant Map
Where this variant sits within the gene, and where the gene sits on the chromosome.
Guess mode is on
The classification and summary are hidden. Take a guess from the gene structure and allele frequency above, then reveal the answer.
In Plain English
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