AI-powered prioritization and interpretation of rare disease variants

VarSage analyzes WES/WGS VCF files (1 Gb max) with HPO phenotype matching, Jannovar annotation, ACMG-style evidence, carrier screening, and optional AI review - generating exportable HTML, CSV, and Microsoft word reports.

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Rare Disease Case Input

Patient name or ID Age in years Sex Expected inheritance

Clinical description (Symptoms or findings) (Required)

AI phenotype extraction

Suggested terms are copied into the HPO fields below. Remove any term that is not supported by the case description.

Present HPO terms (optional)

Absent HPO terms (optional)

Family status Consanguinity reported

Affected relatives (optional)

Family history notes (optional) Human reference BED region filter Variants file upload Variant file type

This file is not VCF. Allow AI to identify the table format and variant columns.

Recommended for CSV, TSV, or unusual annotation exports. The server admin still controls whether AI is available.

Annotation mode

VCF sample ID (if not provided and the VCF file is multi-sample, it takes the first sample in VCF file)

Minimum read depth (DP) Minimum genotype quality (GQ)

AI for this case

Enable AIDisable AI

When enabled, AI may run HPO extraction, optional schema detection, top-ranked variant review, and case synthesis. For reviewed variants, AI may also propose refinements to the provisional ACMG/AMP classification, which are validated by the deterministic evaluator and flagged for expert review. Medical-skills profile: acmg-clinical.

Include rescued variants in AI review

When enabled, clinically strong candidates outside the top-N set (pathogenic/likely-pathogenic assertions, reportability hints, possible same-gene recessive pairs, rare high-impact alleles, strong predictors in phenotype-related genes) are also sent for AI review.

Carrier Screening Input

Couple or case ID Relationship

Clinical / ancestry description Clinical or reproductive notes

AI phenotype extraction

For carrier screening, present terms are used as phenotype-concern HPO terms for gene-scope expansion. Remove terms that are not truly part of the couple's concern.

Present HPO concern terms Absent HPO concern terms

Husband / male partner

Partner ID Age Variant file VCF sample ID

Wife / female partner

Partner ID Age Variant file VCF sample ID

Variant file type For non-VCF partner tables, allow AI to identify variant columns. Annotation mode Genome build

BED region filter

The selected catalog BED regions are applied to both partner files before annotation.

Minimum read depth (DP) Minimum genotype quality (GQ)

AI for carrier screening

Enable AIDisable analysis AI

When enabled, AI may extract concern phenotypes from carrier notes and assist non-VCF table schema mapping when that option is selected. Carrier HTML and Word report narrative still attempts AI drafting whenever the server AI configuration is available.

Carrier screening mode analyzes each partner separately with heterozygous-only filtering, then warns when both retained shortlists contain variants in the same gene.

Trio Analysis Input

Analysis ID Human reference

Proband details

Proband name or ID Proband age in years Proband sex Proband expected inheritance

BED region filter

The selected catalog BED regions are applied to the proband and supplied parent files before annotation.

(Required) Clinical description

AI phenotype extraction

Suggested proband HPO terms are copied into the fields below. Remove any term that is not supported by the submitted clinical description.

Present HPO terms Absent HPO terms

Family status (optional) Consanguinity reported

Family history notes

Proband variant file

Variant file VCF sample ID

Mother

Mother ID Variant file (optional) VCF sample ID

Father

Father ID Variant file (optional) VCF sample ID

Annotation mode

Minimum read depth (DP) Minimum genotype quality (GQ)

AI for trio analysis

Enable AIDisable proband AI

When enabled, AI may run proband HPO extraction, optional schema detection, top-ranked variant review, and case synthesis. Trio HTML and Word report narrative still attempts AI drafting for inheritance and case explanations whenever the server AI configuration is available. Medical-skills profile: acmg-clinical.

Include rescued variants in AI review

Trio mode requires the proband variant file. Mother and father files are optional; supplied parent files enable transmission review, while omitted files are marked as not provided.

AI-powered prioritization and interpretation of rare disease variants

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Analysis Mode

Rare Disease Case Input

Carrier Screening Input

Husband / male partner

Wife / female partner

Trio Analysis Input

Proband details

Proband variant file

Mother

Father

Results

Analysis History