IVA, a locally deployable Intelligent Variant Analyser based on a small language model for complete case-level and trio-based genomic interpretation.

Abstract

Background: Recent work has brought large language models (LLMs) into clinical variant interpretation. In most existing approaches, the model is confined to text-level operations, retrieving, extracting, compacting, and summarizing heterogeneous evidence, while the genuine genetic evaluation is delegated to a separate deterministic engine. Other tools employ LLMs to mine functional evidence for a single ACMG criterion, to rerank a classifier's output, or to answer isolated variant questions. Integrative genetic reasoning, by contrast, demands multi-source evidence weighing for each variant, reconciliation of inheritance with observed zygosity and parental genotypes, joint interpretation of variants in the same gene, and the derivation of a case-level conclusion. Moreover, to protect patient privacy, this must be done on hospital premises. Methods: o build an end-to-end variant interpreter that runs on local infrastructure, we benchmarked 13 small language models (SLMs) on 150 multiple-choice genetics questions and selected Qwen3.5-9B. In IVA (Intelligent Variant Analyser), a four-stage pipeline, the model assigns ACMG/AMP criteria, applies de novo, dominant, recessive, and X-linked inheritance logic to trios, and writes a structured report, while deterministic code handles retrieval, phasing, point summation, citation checking, and formatting. We evaluated IVA on synthetic scenarios, 16 solved trios, and 327 solved singleton cases of visual impairment, on a single GPU. Results: On the benchmark, Qwen3.5-9B reached a mean accuracy of 0.81, compared with 0.89 for a 1.6-trillion-parameter cloud model. In the 16 trios, IVA reported every previously identified pathogenic, likely pathogenic, or uncertain-significance variant of interest (sensitivity 100%; precision 39.5%). In the 327 singleton cases, it recovered 93% of the expert-reported causative variants and classified 82% of them as pathogenic or likely pathogenic (precision 43%). Failures fell into four recurrent classes: omission, unverified mechanism, mismatch between reasoning and label, and arithmetic errors. Conclusions: A small language model running on local hardware can serve as the reasoning layer for case-level and trio-based variant interpretation when it is surrounded by deterministic safeguards. Because its outputs are not deterministic, analyst review and prospective multicenter validation remain necessary.