Query the Genome Aggregation Database (gnomAD). Use when determining the rarity or allele frequency of specific genetic variants, retrieving gene constraint metrics (pLI, LOEUF) to assess loss-of-function intolerance, finding variants in a genomic region or gene, or querying structural variants. Don't use for analyzing individual patient genomes, tracking somatic mutations in cancer (use COSMIC), or requesting raw sequencing reads (use ENA).
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See how to installReview the instructions the agent will receive before you install.
uv: Read the uv skill and follow its Setup instructions to ensure
uv is installed and on PATH.All scripts are located in the scripts/ subdirectory of this skill's
installation directory. When running them, use the full absolute path to the
script (e.g. /path/to/gnomad_database/scripts/get_variant_frequency.py).
1. Variant Frequency. Retrieves global and ancestry-specific allele
frequencies, homozygote counts, and Grpmax Filtering AF (faf95/faf99) for
exome, genome, and total (exome+genome combined) data. The filtering allele
frequency (FAF) is the maximum credible genetic ancestry group AF (lower bound
of the 95% or 99% CI). Variant ID format must be chrom-pos-ref-alt (e.g.,
1-55516888-G-GA). Alternately, you may provide an rsID.
# By variant ID:
uv run scripts/get_variant_frequency.py --variant_id {variant_id} [--dataset {dataset}] --output variant_frequency.json
# By rsID (e.g., rs1800562):
uv run scripts/get_variant_frequency.py --rsid {rsid} [--dataset {dataset}] --output variant_frequency.json
2. Gene Constraint. Retrieves constraint metrics for a gene. The response
will explicitly contain pli, and the LOEUF score is represented by
oe_lof_upper.
uv run scripts/get_gene_constraint.py --gene {gene_symbol} --output {gene_symbol}_constraint.json
3. Region/Gene Variant Search. Finds all variants in a region or gene.
# By region:
uv run scripts/search_variants.py --chrom {chrom} --start {start} --end {end} --output region_variants.json
# By gene:
uv run scripts/search_variants.py --gene {gene_symbol} --consequence {pLoF|missense} --output {gene_symbol}_variants.json
Further documentation on the data: https://gnomad.broadinstitute.org/data#api More general database documentation: https://gnomad.broadinstitute.org/help
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Retrieve and analyze AlphaFold predicted structures for a protein. Use when the user provides a specific UniProt Accession ID and wants structural confidence metrics (pLDDT), domain boundary analysis, or disorder assessment. Do not use if the user only has a protein name, gene name, or amino acid sequence — ask for a UniProt ID first.
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Constructs deep-links and URLs for the AlphaGenome Atlas website. Supports generating single-variant exploration links (1-based chr:pos:ref>alt), genomic locus views (1-based closed chr:start-end), candidate summary tables, and AlphaGenome reference vs. alternate predictions. Use whenever visualizing, exploring, charting, or linking genetic variants and genomic loci on the AlphaGenome Atlas, or when asked to inspect, view, or link predictions for a genomic variant.
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Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API. Use when the user asks about non-coding variant effects, pathogenicity, clinical significance, disease associations, functional effects, gene expression changes, splicing disruption, or regulatory effects in promoters and enhancers. Also use for resolving biological terms to tissue/cell-type ontologies (UBERON/CL) or analyzing variants in chr:pos:ref>alt format.
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Score, annotate, and analyze the functional impact of genetic variants using AlphaGenome Variant Impact (AVI) scores. Query variants in chr:pos:ref>alt format, annotate VCF/tabular callsets, perform saturation mutagenesis window scans (1-based closed chr:start-end), and extract GENCODE v46 GTF gene/exon/junction coordinates all via the AlphaGenome Atlas API.
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Query the ChEMBL database for bioactive molecules, drug targets, bioactivity data, approved drugs, and chemical structures. Use when the user asks about compounds, targets, IC50/Ki values, drug mechanisms, or structure searches.
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Query ClinicalTrials.gov via APIv2. Use when you want to search for trials by condition, drug, location, status, or phase; retrieve trial details by NCT ID; check eligibility/inclusion criteria; count trials across conditions or time periods; identify a sponsor's trial portfolio; find recruiting trials for patient matching.
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