VS Code gnomad genetics mcp server Prompt/gnomad_variant_triage
How to: VS Code gnomad genetics mcp server gnomad_variant_triage
Add gnomad genetics mcp server to VS Code
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01
Open .vscode/mcp.json and merge this in. Keep any servers already there.
{
"servers": {
"gnomad-genetics-mcp-server": {
"type": "http",
"url": "https://gnomad-genetics.caseyjhand.com/mcp"
}
}
}-
02
Save the file and restart VS Code.
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03
gnomad_variant_triage is surfaced in the client's prompt or command menu. Unlike a tool, you invoke it deliberately — VS Code will not call it for you.
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04
If it does not appear, check that gnomad genetics mcp server is connected and that you are looking at its prompts rather than its tools.
Requires agent mode. MCP: Open User Configuration puts the same block in every workspace. VS Code docs
Set these first
gnomad genetics mcp server will not start until these are set, so it never reaches VS Code.
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MCP_LOG_LEVEL
Same prompt, other clients
Read from the server itself, by connecting to it and calling prompts/list on 24 September 2026.
A listing does not declare its prompts, so asking is the only way to know them, and this
is what the server actually offers rather than what its listing claims. Names only are
stored; connect the server for each prompt's arguments.