0%
complete
Final classification
VUS
PM2
ATM
c.7243G>C
p.Ala2415Pro
missense · exon 49

ATM encodes a kinase that acts as a master controller of the cellular DNA damage response: it detects double-strand breaks and coordinates DNA repair, cell cycle arrest, or apoptosis through downstream targets including p53, BRCA1, and CHK2. Loss-of-function mutations in both copies of ATM cause ataxia telangiectasia, an autosomal recessive disorder characterized by neurological problems, immune deficiency, and cancer predisposition. ATM functions as a tumor suppressor: individuals with ataxia telangiectasia are prone to childhood lymphomas, leukemias, and breast cancer, while carriers of a single altered copy have increased risk of breast, pancreatic, prostate, and other cancers. Somatic ATM mutations also occur in lymphoid malignancies and solid tumors, and ATM-deficient cancers are often especially sensitive to DNA-damaging treatments.

This variant

This missense change is classified as a VUS, meaning it neither establishes nor excludes ATM-related disease. Because loss of ATM function causes ataxia telangiectasia and raises cancer risk in carriers, this variant's extreme rarity alone cannot establish pathogenicity, and functional or segregation evidence is still needed.

Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.7243G>C
GRCh38
chr11:108329174 G>C
GRCh37
chr11:108199901 G>C
PM2 (Supporting) is the only criterion met; with no pathogenic or benign combination rule satisfied, the variant is classified VUS.
Classification rationale
PM2 VUS
ATM c.7243G>C missense · exon 49

PM2 (Supporting): absent from gnomAD v4.1, satisfying the <=0.001% rarity threshold. Overall classification: VUS, as the sole PM2 (Supporting) criterion satisfies no pathogenic or benign combination rule.

PM2 VUS
Gene diagram · NM_000051.4 · variants mapped to exon structure
ATM NM_000051.4
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 13 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
Met (Supporting): absent from gnomAD v4.1, satisfying the <=0.001% PM2 rarity threshold.
ClinGen HBOP ATM VCEP v1.5 PM2 rule: frequency <=0.001% in the gnomAD v4 dataset, applied as PM2_Supporting rather than moderate.The gnomAD v4.1 lookup for chr11:108329174 G>C returned search_status=absent, corresponding to no observed alternate allele in the supplied result.The variant was also reported absent from gnomAD v2.1 and gnomAD-Canada v1.0; no homozygote or ancestry-specific frequency was reported.
Assessed · not applied · 7 not met · 6 not assessed
Pathogenic
PVS1 Not met: p.Ala2415Pro is a missense change, not a null variant, and SpliceAI max delta 0.012 shows no splice impact.
PS1 Not met: no pathogenic comparator with the same p.Ala2415Pro change exists; the only ClinVar entry is a single-submitter VUS.
PS3 Not assessed: a research screen predicts loss of function, but it is not a VCEP-approved assay and awaits human review.
PS4 Not assessed: no case-control enrichment study for this exact variant was identified.
PM3 Not assessed: no affected proband, second ATM variant, or phase/in-trans evidence was documented.
PM4 Not met: PM4 is restricted to stop-loss variants, and p.Ala2415Pro does not alter protein length.
PP1 Not assessed: no segregation data in affected relatives were available for this variant.
PP3 Not met: REVEL 0.512 falls below the >0.7333 threshold and SpliceAI max delta 0.012 below 0.2.
Benign
BA1 Not met: absent from gnomAD v4.1, far below the >0.5% stand-alone benign frequency threshold.
BS1 Not met: absent from gnomAD v4.1, below the >0.05% BS1 frequency threshold.
BS3 Not assessed: no validated benign functional result was available; the research assay instead predicts loss of function.
BP2 Not assessed: no qualifying unaffected-carrier co-occurrence or phase data were available.
BP4 Not met: REVEL 0.512 exceeds the <=0.249 threshold required by the laboratory's missense BP4 rule.
N/A · 14 PS2 · PM1 · PM5 · PM6 · PP2 · PP4 · PP5 · BS2 · BS4 · BP1 · BP3 · BP5 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 1757879)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.512. BayesDel score = 0.177845.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. ATM, a kinase involved in the DNA damage response, is mutated in various solid and hematologic malignancies.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 1 PMID not cited in assessment
25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR