c.5178-28T>A is a rare deep intronic variant in ATM, located 28 bp upstream of the exon 35 acceptor splice site, that is absent from all queried population databases including gnomAD v2.1, v4.1, and gnomAD-Canada (>800,000 alleles screened).

SpliceAI in silico analysis predicts a potential splicing impact with a max delta score of 0.27 (DS_AL=0.27, DS_DL=0.26), exceeding the ATM VCEP 1.5.0 threshold of ≥0.2, consistent with the possible creation of an alternative splice acceptor or donor site.

The variant has not been reported in ClinVar and no functional studies (RNA splicing assays, ATM kinase activity, or radiosensitivity testing) have been published; thus no functional confirmation of the predicted splicing effect is available.

No A-T probands carrying this variant in trans with a pathogenic ATM variant have been reported, leaving the PM3 criterion unevaluable. Similarly, no cosegregation data (PP1) or case-control enrichment data (PS4) exist for this variant.

Applying the ATM VCEP 1.5.0 framework, two supporting-level pathogenic criteria are met: PM2_Supporting (absence from population databases) and PP3 (SpliceAI splicing prediction). No benign criteria are met. Under the ACMG/AMP 2015 combining rules adopted by the ATM VCEP, two supporting pathogenic criteria without any moderate, strong, or very strong criteria are insufficient to reach Likely Pathogenic. The variant is classified as a Variant of Uncertain Significance (VUS).

Resolution of this VUS would require: (1) RNA functional studies (RT-PCR or minigene assay) to confirm or exclude aberrant splicing, which could upgrade PVS1_Strength(RNA) or support BP7_RNA; (2) identification of the variant in trans with a pathogenic ATM variant in an A-T proband for PM3; and (3) reporting of this variant to ClinVar with clinical phenotype data.