variant-report

name	variant-report
description	Generate a variant annotation report combining Ensembl, ClinVar, and UniProt data for a gene or genomic region

Generate a comprehensive variant annotation report for: $ARGUMENTS

Use the MCP tools available to you to gather variant data from all relevant sources, then synthesize a single structured report. Follow the steps below. If a step fails, note the gap and continue.

Determine Input Type

First, classify the input:

• Gene symbol (e.g., TP53, BRCA1): Look up genomic coordinates first, then find variants in that region.
• Genomic region (e.g., 7:140453136-140453236): Use directly for variant lookup.
• Specific variant (e.g., NM_007294.4:c.5266dupC or rs ID): Search ClinVar directly.

Data Gathering Steps

For Gene Symbol Input:

1. Gene Coordinates

• Call ensembl_lookup_gene with the gene symbol to get chromosomal coordinates.
• Note the chr:start-end for variant queries.

2. Known Variants in the Region

• Call ensembl_get_variants with the gene's region (species: homo_sapiens, limit: 100).
• Summarize: total variants found, breakdown by consequence type, any with clinical significance.

3. ClinVar Annotations

• Call clinvar_search with the gene symbol (limit: 20) to get clinical interpretations.
• Call clinvar_search with "[gene] AND pathogenic" to specifically find pathogenic variants.
• Summarize: total entries, breakdown by clinical significance (pathogenic, likely pathogenic, VUS, benign).

4. Protein Feature Context

• Call uniprot_search with the gene symbol and organism_id:9606 (reviewed: true) to find the UniProt accession.