clinical-genetics

Clinical genomics web app to visualize & prioritize exome VCF variants on protein structures — published in Bioinformatics (2019)

ACMG Assistant is a student-level, research-oriented variant classification tool developed to explore the practical application of ACMG/AMP 2015 and 2023 guidelines. It combines automated retrieval of annotation data from public APIs with structured interactive evidence collection to support systematic variant interpretation.

MCP gateway federating 21 biomedical MCP servers — gnomAD, ClinVar, HPO, UniProt, Ensembl VEP, PanelApp and more — behind one Streamable-HTTP endpoint, with collision-free namespaced tools and BM25 tool search.

Calibrate functional/in-silico variant scores into ACMG clinical evidence strengths (ClinGen-SVI), with LDLR/AlphaMissense worked example

Drafts ACMG/AMP variant classifications for a human curator: gathers genomics evidence, adjudicates each criterion with Claude, computes the label in code via ClinGen points, and shows every source.

Triages inconclusive genetic variants: reconciles AlphaMissense predictions against ClinVar assertions on AlphaFold structure, and grades how much evidence backs each call.

Mechanism-aware variant interpretation pipeline for monogenic epilepsy: RF + ESM-2 LoRA pathogenicity heads, gain-vs-loss-of-function mechanism classifier, sodium-channel prescribing rule, leave-one-out dynamic-evidence framework.

MCP server for GeneReviews: the expert-authored, peer-reviewed gene–disease chapters on NCBI Bookshelf, served as a searchable corpus of individually citable passages.

Research tool for exploring carrier frequencies and recurrence risks for autosomal recessive conditions using gnomAD population data. For research use only.

Interactive web-based tool for visualizing gene variants, protein domains & annotations – no coding required. Customize maps, highlight variants, export SVG/PNG.

MCP server for PanelApp: consensus diagnostic gene panels and gene–disease ratings from Genomics England (UK) and PanelApp Australia — as typed tools for LLM agents.

MCP server for NCBI ClinVar: variant clinical significance and gene-level classifications, served from a local SQLite index built from the ClinVar weekly bulk release — not the eUtils API.

MCP server for AutoPVS1: automated ACMG PVS1 loss-of-function evidence for sequence variants and copy-number variants — variant interpretation as typed tools for LLM agents.

MCP server for GenCC (Gene Curation Coalition): harmonized gene–disease validity classifications across member submitters, with consensus and conflict detection per gene–disease pair.

MCP server for ClinGen (Clinical Genome Resource): gene–disease validity, dosage sensitivity, clinical actionability, and expert-panel variant pathogenicity (ERepo) — as typed tools for LLM agents.