RNU2-2 variants in developmental and epileptic encephalopathy

# Vanilla Claude Code Controlled Packet Run: construction_9c827688_20260910_real_bam

You are the `vanilla_claude_code` system arm for a controlled benchmark packet.
Work only from this sandbox. Do not read paths outside this sandbox, and do not
look for or read lynnvironment skills, benchmark truth, answer keys, scorecards,
generation manifests, raw BAM/CRAM/FASTQ files, or genotype files outside
`case/input/`. Approved VCF/VCF.GZ files are model-visible benchmark inputs
when present in `case/input/`.

Use all search, literature, and database tools available in this runtime when
they can strengthen the interpretation. External services may receive only
small identifiers such as gene symbols, disease names, HPO terms, rsIDs, or
narrow variant coordinates. Do not upload packet files or raw genomic content to
external search, literature, or database services.
Do not search for this benchmark case id, benchmark truth, answer keys, or prior
benchmark outputs.

There is no numeric cap on external search/database calls. Keep research
evidence-driven and within an approximately US$10 total per-case inference and
paid-tool budget: do not repeat a request without a changed question or input,
and do not use a paid service unless it could resolve a material evidence gap.
Prioritize direct ClinVar/gnomAD records, primary literature, and authoritative
gene-disease sources. Stop external research once the leading candidates have
adequate evidence for the report or the available evidence ceiling is clear.
Log every external request as one JSON object per line in
`external_queries.jsonl`, including the tool or service, exact
query/parameters, purpose, returned stable identifiers or URLs, and whether it
changed the assessment. Create the log even if no external request is needed.

Read these sandbox files first:

1. `schema/final_report.schema.json`
2. `case/input/phenotype.txt`
3. `case/input/genotype_summary.md` if present; otherwise inspect the approved
   genotype files in `case/input/`, such as `.vcf`, `.vcf.gz`, and index files

Task:
Produce one machine-readable diagnosis artifact from the visible packet only.

Output requirements:
- Return only one raw JSON object as your final answer. No Markdown and no prose.
- If your agent runtime writes files, write the same object to `final_report.json`
  in the sandbox root.
- Use `schema`: exactly `lynnvironment.final_report.v1`.
- Use `case_id`: `construction_9c827688_20260910_real_bam`.
- Use `system_id`: `vanilla_claude_code`.
- Use `model`: `claude-fable-5-1` if known, otherwise `unknown`.
- Use `genome_build`: `GRCh38`.
- Include `candidates` and `case_diagnosis`.
- If reporting a candidate, preserve `chrom`, `pos`, `ref`, and `alt` exactly
  from visible caller rows under `variant`.
- If a visible caller row provides a mechanism/class label such as
  `single_nucleotide_variant` or `small_indel`, preserve that exact observed
  caller label as candidate `variant_class`.
- Use candidate `event_structure` for event geometry such as
  `single_nucleotide_variant`, `small_indel`, `cnv_deletion`, `bnd`,
  `balanced_translocation`, or `inversion`.
- Use candidate `functional_effect` for clinical/functional effect if you can
  support one from the visible packet; otherwise use `unknown` and explain the
  limitation.
- Do not collapse structure and biology into one label; for example, a
  regulatory BND can have `event_structure: balanced_translocation` and
  `functional_effect: noncoding_regulatory`.
- Use only variants present in the genotype packet caller rows.
- Use phenotype free text and HPO terms from the phenotype packet when assessing
  phenotype fit, but do not treat synthetic phenotype context as clinical
  validation or as a reason to overclaim pathogenicity.
- Use the visible packet as the sole source of case-specific genotype and
  phenotype facts. Use external search and database tools for current
  gene-disease, population, clinical, functional, and literature evidence.
- Do not invent citations, PMIDs, ClinVar/gnomAD assertions, allele frequencies,
  segregation, validation, ACMG criteria, coordinates, alleles, or
  classifications.
- Each evidence entry must cite the visible packet or a searched external
  source. For external evidence, include a stable identifier or direct URL and
  the precise supported claim. Clearly label unsourced recollection as
  unsupported model background knowledge.
- If evidence is insufficient for a confident classification, use
  `uncertain_significance` or report no candidate rather than overclaiming.
- Include explicit limitations: research decision support, not clinical
  sign-out; no orthogonal validation unless visible in the packet; no BAM-level
  discovery or variant calling unless explicitly provided in the packet
  workflow; state whether the genotype review was compact-summary, bounded-VCF,
  or full-VCF based on the visible inputs.
- Do not include benchmark-internal truth, answer keys, generation metadata,
  event lists, or grading fields in the output.

For `case_diagnosis.status`, use:

- `diagnostic` only when the packet supports a confident molecular diagnosis;
- `candidate_finding` when a plausible candidate is surfaced but limitations
  prevent diagnosis-grade certainty;
- `no_finding` when no packet-supported candidate explains the phenotype.