Variant Explorer¶

Not a medical test — for research and educational use only

Yeliztli analyses consumer genotyping-array data (23andMe / AncestryDNA), which is not a clinical-grade test. Results are not diagnostic, are not clinically validated, and must not be used to make medical decisions. Array data is especially unreliable for rare, disease-causing variants. Always confirm any finding with an accredited clinical laboratory and discuss it with a qualified clinician or genetic counsellor before acting on it. See the Intended use & disclaimers page for the details and the evidence behind this warning.

The Variant Explorer is the central table for browsing every variant in your sample.

Chromosome anchors — jump to any chromosome from the navigation bar.
Infinite scroll — variants load progressively as you scroll.
Total count — shown asynchronously, so the first page appears immediately. By default this is the table count after hiding rows with missing annotation state; turn on Show unannotated to include those rows. This is separate from the dashboard's full uploaded-position count, which includes no-calls.

Filtering¶

Toggle Show unannotated to include rows whose annotation coverage is still missing.
Use the advanced filter panel for specific criteria — gene, consequence, allele frequency, ClinVar significance, and more.
Search ClinVar significance for conflicting to review variants ClinVar marks as Conflicting classifications of pathogenicity; these variants are not shown as pathogenic-variant findings.
Filter by the tags you've applied (see below).

Column presets¶

Switch between predefined column layouts, or build your own from Column Settings:

Preset	Columns shown
Clinical	Genotype, Gene, Consequence, ClinVar significance, ClinVar review stars
Research	Genotype, Gene, Consequence, ClinVar significance, ClinVar review stars, CADD, SIFT score/prediction, PolyPhen-2 score/prediction, REVEL, ensemble pathogenic flag
Frequency	Genotype, Gene, global gnomAD AF, rare flag
Scores	Gene, Consequence, CADD, SIFT score/prediction, PolyPhen-2 score/prediction, REVEL

Coordinates & assembly (GRCh37 / GRCh38)¶

The default Chr and Position columns are GRCh37 (hg19) — the app's native assembly, which every uploaded sample is normalised to. A toolbar GRCh38 toggle adds two extra columns, Chr (GRCh38) and Pos (GRCh38), so a variant's coordinate is shown in both assemblies side by side:

The GRCh38 columns are a computational liftover of the native GRCh37 coordinates, added for looking a variant up in GRCh38-based external tools — not an independent source of truth (a liftover can be wrong or fail).
A blank GRCh38 cell means the position could not be lifted over: either the region was deleted or rearranged between GRCh37 and GRCh38, or the variant is mitochondrial (MT is deliberately never lifted — the UCSC hg19 chrM is the old Yoruba reference sequence, not the rCRS the chip data uses, so lifting it would give wrong GRCh38 coordinates).
Which to use: paste the default (GRCh37) coordinate into GRCh37/hg19-based tools and the GRCh38 coordinate into GRCh38/hg38-based tools. Two differing Position numbers for one variant are expected — it is the same variant in two assemblies.

Tagging¶

Apply tags to variants for personal tracking — predefined ones (Pathogenic interest, Benign confirmed, Follow-up, Research) or your own. You can then filter the table by tag.

Custom annotation overlays¶

Use Annotation Overlays to upload small BED or VCF files and compare custom annotations with your sample's variants. Overlay matches are display-only: they help triage variants, but they do not change findings, scores, or evidence ratings.

Watching a VUS¶

For a Variant of Uncertain Significance, click Watch. When reference databases are updated, watched variants are re-checked and you're notified if any are reclassified.

Click any row to open the variant detail panel. Gene symbols link to the full Gene Detail page for that gene.