Classification rationale
PM5PM2PVS1
Pathogenic
ATM c.4300A>T
The ATM c.4300A>T (p.Lys1434Ter; p.K1434*) variant has not been observed in somatic cancers in COSMIC and has not been reported in ClinVar.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, placing it below the ATM VCEP PM2_Supporting threshold of 0.001% and well below the BS1 (>0.05%) and BA1 (>0.5%) thresholds.2 This is a nonsense variant predicted to introduce a premature stop codon at Lys1434; SpliceAI predicts no significant splice impact with a maximum delta score of 0.03, supporting interpretation as a truncating loss-of-function event rather than a splice-altering event.3
PM5 + PM2 + PVS1
→
Pathogenic
3
spliceai ↗pvs1_variant_assessmentvcep_atm_pvs1_1_5cspec ↗