The NM_000156.6:c.459+9_459+12del variant in GAMT is an intronic variant that is located in intron 4 and leads to a deletion of 4 base pairs. The highest popualtion minor allele frequency in gnomAD v2.1.1 is 0.00006166 (1 in 16218 alleles) in the African population which is lower than the ClinGen CCDS VCEP’s threshold for PM2_Supporting (<0.0004), meeting this criterion (PM2_Supporting). The computational predictor SpliceAI suggests that this variant has no impact on the gene/gene product (BP4). There is a ClinVar entry for the variant (Variation ID: 513151). Due to conflicting evidence, this variant is classified as a variant of unknown significance for GAMT deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen Creatine Deficiency Syndromes Variant Curation Expert Panel (Specifications Version 1.1.0): BP4, PM2_Supporting. (Classification approved by the ClinGen CCDS VCEP on June 6, 2022).