About gnomAD (population variant frequencies)
The Genome Aggregation Database from the Broad Institute. Get a gene’s constraint metrics (pLI, LOEUF), its observed variants with allele counts and frequencies per population, filtered by consequence, or one variant by rsID. CC0 data; the BY-NC SpliceAI annotation is not exposed.
Questions you can ask gnomAD
Type them into Kahubi’s chat once gnomAD is connected.
“How constrained is SCN2A against loss-of-function variants?”
What comes back: pLI, LOEUF and missense z-score, plus ClinVar variants with significance and review stars.
“What is the allele frequency of rs80357906 across populations?”
What comes back: Exome and genome allele counts and frequencies, homozygote counts and per-population frequencies.
gnomAD MCP tools
The 3 tools the gnomAD server offers to Kahubi. The assistant picks the right one for each question.
gnomad_geneGene summary: Ensembl id, coordinates, constraint metrics (pLI, LOEUF = oe_lof_upper, missense z) and ClinVar variants with significance and review stars.
gnomad_gene_variantsObserved gnomAD variants in a gene with allele counts and frequencies.
gnomad_variantOne variant by rsID (rs80357906) or gnomAD id (17-43057062-T-TG): exome and genome allele counts and frequencies, homozygotes, per-population frequencies, transcript consequences.
Using gnomAD in Kahubi
- Hosted by Kahubi. Kahubi runs this server itself so it stays reliable enough for research use.
- Cited, checkable answers. Results are treated as retrieved material and cited with the source’s own identifiers, so you can open every record the answer relied on.
- Your files stay private. Only the search the assistant writes for your question is sent to gnomAD.
More life science sources
- TogoMCP (UniProt, ChEMBL, PubChem, PDB, Reactome, NCBI)One service across 30+ life-science databases: proteins, genes, compounds, structures, pathways, variants and MeSH.
- Open Targets PlatformTarget–disease–drug associations with the evidence behind them, from EMBL-EBI.
- Protein structures (PDB, AlphaFold)Search experimental and predicted protein structures, find similar folds, track ligands and fetch annotations.
- NCBI E-utilitiesGene, ClinVar, dbSNP, Taxonomy, Nucleotide, Protein, PMC and other NCBI databases.
- GBIF (biodiversity occurrences)2.5 billion species occurrence records from museums, surveys and citizen science worldwide.
- iNaturalistCitizen-science observations with photos, research-grade identifications and places.