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Variant detail

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.

Click any variant in the Variant Explorer to open a side panel with a summary, then Open full detail for the full page, organised into tabs:

  1. Overview — genomic location, HGVS notation, and transcript details (the MANE Select transcript is flagged), a ClinVar summary, and a Key Scores block: gnomAD global allele frequency with a rare / ultra-rare flag, plus CADD, REVEL, SIFT, and PolyPhen-2.
  2. Population — gnomAD allele frequencies across subpopulations (Global, African, Latino/Admixed, Ashkenazi Jewish, East Asian, European, Finnish, South Asian), the gnomAD homozygote count, and a rarity note.
  3. Protein — the variant's protein change (HGVS p.) and a link to the gene's full Gene Detail page, where the Nightingale protein-domain diagram is rendered. The diagram is not shown inline here, and this page does not mark the variant's position on it.
  4. Clinical — the ClinVar record (clinical significance, review stars, accession, and reported conditions), any evidence-conflict callout, the full in-silico prediction panel (CADD, SIFT, PolyPhen-2, REVEL, MutPred2, VEST4, MetaSVM, MetaLR, GERP++, phyloP, MPC, PrimateAI, plus an ensemble-pathogenic flag), GTEx eQTL and SpliceAI context badges, and gene–disease associations (MONDO/HPO, plus OMIM if you've added a key).
  5. Literature — planned; not yet implemented. A per-variant PubMed literature search (keyed by gene and phenotype) is slated for a future release; today this tab shows a placeholder only. (PubMed literature is used elsewhere — for clinical findings — but is not wired into this tab.)
  6. Genome — an embedded IGV view of a ~10 kb window around the variant with the default annotation tracks, plus a link into the full Genome Browser.

You can jump straight to the variant in the Genome Browser. Single-variant evidence-card exports are not currently surfaced from the variant detail page; the backend variant-card endpoints are keyed to reportable findings rather than arbitrary Variant Explorer variants.

Understanding HGVS notation

The Overview and Protein tabs name the variant in HGVS notation — the international standard for describing sequence variants.1 It appears as two strings:

  • Coding (c.) — the change on the gene's coding-DNA reference sequence; > marks a single-base substitution. So c.665C>T means "at coding-DNA position 665, the reference base C is replaced by T."
  • Protein (p.) — the predicted amino-acid change, written with three-letter amino-acid codes. So p.Ala222Val means "at protein position 222, Alanine is replaced by Valine."

Both describe the same variant — one at the DNA level, one at the protein level. The numbers are relative to the variant's transcript (the MANE Select transcript is flagged in the Overview tab), so the same change can carry different c. / p. numbers on different transcripts. See the HGVS nomenclature reference for the full rules.

  1. HGVS Recommendations for the Description of Sequence Variants: 2016 Update (den Dunnen et al., 2016, Human Mutation; PMID 26931183) defines the international standard nomenclature for sequence variants, including the c. (coding-DNA) and p. (protein) prefixes. ↩