Variant classification challenges in genes associated with multiple disorders contribute to the persistent interlaboratory discordance

Background Accurate germline variant classification requires correct application of ACMG/AMP evidence criteria and assignment of pathogenicity to a specific disease entity and mode of inheritance. Whether laboratories apply this disease-specific approach consistently to genes associated with multiple disorders remains insufficiently characterized. Methods We conducted a national interlaboratory study of germline variant classification using a proficiency-testing dataset comprising 13 variants across five clinical scenarios from 128 Chinese clinical genetic laboratories. Results Overall concordance was achieved for 6 of 13 variants, whereas 7 showed clinically meaningful cross-category discordance. Residual disagreement was partly attributable to omission or inappropriate use of ACMG/AMP evidence criteria, inconsistent strength assignment, and disease-context-specific interpretation. A prominent pattern of discordance involved disease-specific interpretation of variants in genes associated with multiple disorders. For variants in APOB , LZTR1 , MYH7 , and EPCAM , laboratories frequently transferred pathogenic assertions across disorders without adequately considering disease mechanism, inheritance pattern, or disorder-specific validity. By contrast, two GJB2 variants showed substantially higher categorical concordance. These errors could alter downstream clinical interpretation and, in some cases, implied management recommendations. Conclusions Disease-specific classification in multi-disease genes remains an important source of residual discordance despite improved criterion-level harmonization. Harmonization efforts should therefore extend beyond gene-level pathogenicity assessment toward mechanism-aware, disease-anchored classification frameworks and reporting practices. Clinical trial number Not applicable.