NM_000489.5:c.7315C>A (p.Pro2439Thr) is a missense variant in exon 35 of the ATRX gene. This variant is absent from gnomAD v2.1 and v4.1 (PM2_Supporting).¹ Multiple lines of computational evidence suggest no deleterious effect: BayesDel score of -0.166588 is in the benign range, and SpliceAI predicts no splicing impact (max delta = 0.00) (BP4_Supporting).² A clinical testing laboratory (Invitae/Labcorp) has classified this variant as Likely benign in ClinVar (SCV002431510, criteria provided, single submitter) (BP6_Supporting). Caution: the ClinVar record matched to a different transcript version (NM_000489.6:c.7429C>A vs NM_000489.5:c.7315C>A), though these likely represent the same genomic variant.³ Under generic ACMG/AMP 2015 classification rules (PMID:25741868), the combination of two supporting benign criteria (BP4, BP6) meets the threshold for Likely Benign, despite one supporting pathogenic criterion (PM2).⁴