NM_000051.4:c.662+13_662+14del is an intronic deletion in ATM intron 6 at positions +13 and +14 relative to the exon 6 donor site.

SpliceAI predicts no significant splice impact for this variant (max delta score 0.05), qualifying for BP4_Supporting per VCEP threshold of ≤0.1.

The variant is located at +13/+14, beyond the VCEP BP7 deep intronic cutoff of +7, with no predicted aberrant splicing, qualifying for BP7_Supporting.

This variant is present in gnomAD v4.1 at an extremely low allele frequency of 0.00012% (2/1,613,430 alleles, no homozygotes), meeting the VCEP PM2_Supporting threshold of ≤0.001%. It is absent from gnomAD v2.1.

This variant has been reported in ClinVar as Likely benign by 3 clinical laboratories (VariationID 421805), though the VCEP does not permit use of BP6/PP5.

No functional studies, case-control data, segregation data, or co-occurrence observations have been identified for this variant in the published literature.

Per the ATM HBOP VCEP v1.5.0 framework, two benign supporting criteria (BP4, BP7) are met, resulting in a classification of Likely Benign (Richards et al. 2015 Rule 19: ≥2 Benign Supporting → Likely Benign).