Introduction:
The ClinGen Galactosemia Variant Curation Expert Panel (VCEP) has developed variant classification criteria for the gene GALT and is currently piloting these rules. Throughout criteria creation, the VCEP encountered several challenges related to evidence codes, hypomorphic variants, and populations with underrepresented genomic information.

Methods:
The Galactosemia VCEP has established gene-specific ACMG/AMP guidelines for the interpretation of GALT sequence variants. These criteria were created via in-depth literature review and discussion as a multidisciplinary panel with a diverse representation of institutions. The VCEP is now in pilot phase, during which, a collection of GALT variants with previously established classifications will be curated using our gene-specific guidelines. The curation process involves a comprehensive literature review and collaboration among panel members to reach a consensus on variant classification.

Results:
During consideration of disease-specific allele frequency cut-offs, multiple approaches were compared, with the outcome of excluding some pathogenic founder variants from satisfying PM2 criteria. Also, we propose biochemical testing results (RBC GALT enzyme activity <10%) be used to meet phenotype evidence (PP4_Moderate) based on the range at which clinical features manifest and based on the ACMG technical guidelines for galactosemia; this threshold will continue to be reexamined as we continue our pilot study.

Conclusion:
Significant challenges have been encountered during criteria creation and piloting. One concern is addressing common hypomorphic variants that require unique considerations. There is inconsistency in the field regarding the D2 Duarte haplotype as individuals with this haplotype and a pathogenic variant in trans can present with biochemical perturbations, but are not at risk for clinical disease. One variant in the haplotype is c.-119_116delGTCA and the classifications for this variant in ClinVar are discrepant (pathogenic/likely pathogenic, uncertain significance, and “Other”). A compounding problem is that profoundly pathogenic variants can co-exist in cis with D2 variants, and due to only targeting the D2 Duarte variant, these variants can be missed during testing, leading to mis-interpretation. Another challenge is posed by c.404C>T (p.Ser135Leu) which is common in patients of African, Brazilian, and Portuguese ancestry, who are under-represented in the biomedical literature.This variant is associated with disease, but patients tend to have milder long-term outcomes. While similar variant-specific issues have been encountered by other Inborn Errors of Metabolism (IEM) VCEPs (e.g., pseudodeficiency alleles in GAA), these GALT variants will need novel approaches to variant interpretation within an ACMG/AMP framework. The VCEP will discuss their classification criteria for GALT as well as the challenges encountered.