Initial release: rarelens platform skeleton (AGPL-3.0)

End-to-end variant interpretation platform for rare genetic disease research:
SvelteKit UI, FastAPI + PostgreSQL API, Nextflow/Ensembl VEP pipeline,
LightGBM pathogenicity scoring with MLflow, K8s/ArgoCD/GCP infrastructure.
Public test data only; no clinical claims.

api/app/routers/variants.py

@@ -0,0 +1,43 @@
+import uuid
+
+from fastapi import APIRouter, Depends, Query
+from sqlalchemy import func, select
+from sqlalchemy.ext.asyncio import AsyncSession
+from sqlalchemy.orm import selectinload
+
+from app.db import get_session
+from app.models import Prediction, Variant
+from app.schemas import VariantPage
+
+router = APIRouter()
+
+
+@router.get("", response_model=VariantPage)
+async def list_variants(
+    job_id: uuid.UUID,
+    gene: str | None = None,
+    impact: str | None = Query(None, pattern="^(HIGH|MODERATE|LOW|MODIFIER)$"),
+    max_af: float | None = Query(None, ge=0, le=1),
+    min_score: float | None = Query(None, ge=0, le=1),
+    limit: int = Query(50, le=500),
+    offset: int = 0,
+    session: AsyncSession = Depends(get_session),
+):
+    stmt = select(Variant).where(Variant.job_id == job_id)
+    if gene:
+        stmt = stmt.where(Variant.gene == gene.upper())
+    if impact:
+        stmt = stmt.where(Variant.impact == impact)
+    if max_af is not None:
+        stmt = stmt.where((Variant.gnomad_af.is_(None)) | (Variant.gnomad_af <= max_af))
+    if min_score is not None:
+        stmt = stmt.join(Prediction, Prediction.variant_id == Variant.id).where(Prediction.score >= min_score)
+
+    total = await session.scalar(select(func.count()).select_from(stmt.subquery()))
+    rows = await session.scalars(
+        stmt.options(selectinload(Variant.prediction))
+        .order_by(Variant.chrom, Variant.pos)
+        .limit(limit)
+        .offset(offset)
+    )
+    return VariantPage(items=rows.all(), total=total or 0, limit=limit, offset=offset)