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NM_000051.4:c.3332T>C
p.Leu1111Pro · ATM
0%
complete
Final classification
VUS
PM2
ATM
c.3332T>C
p.Leu1111Pro
missense · exon 23

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

ATM is a tumor suppressor whose loss of function causes ataxia telangiectasia and raises cancer risk in carriers. This missense change is classified as a variant of uncertain significance: it is extremely rare in the general population, but no functional, segregation, or clinical evidence currently shows it impairs ATM's DNA-damage-response function or predisposes to disease.

Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.3332T>C
GRCh38
chr11:108279538 T>C
GRCh37
chr11:108150265 T>C
Only PM2 (supporting) was met under the ATM VCEP v1.5 criteria-combination framework - insufficient evidence for any pathogenic or benign classification.
Classification rationale
PM2 VUS
ATM c.3332T>C missense · exon 23

PM2 (Supporting): gnomAD v4.1 allele frequency 0.00031% (3.1e-06), below the <=0.001% threshold, with no observed homozygotes. Overall classification: VUS - only PM2 (Supporting) was met, insufficient for any pathogenic or benign rule under the ATM VCEP v1.5 combination framework.

PM2 VUS
LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
Gene diagram · NM_000051.4 · variants mapped to exon structure
ATM NM_000051.4
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 11 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): gnomAD v4.1 allele frequency 0.00031% (3.1e-06), below the <=0.001% PM2 threshold, with no observed homozygotes.
ClinGen HBOP ATM VCEP v1.5 specifies PM2_Supporting at frequency <=0.001% in gnomAD v4.1 and states that n=1 in a single subpopulation is sufficiently rare.gnomAD v4.1 reports 5/1,613,720 alleles overall (AF 3.09843e-06; 0.000309843%), a highest population AF of 4.237877e-06 in European non-Finnish individuals (5/1,179,836), grpmax FAF 1.24e-06, and zero homozygotes.The variant is absent from gnomAD-Canada v1.0, providing additional population rarity context without changing the VCEP threshold assessment.
Assessed · not applied · 5 not met · 6 not assessed
Pathogenic
PS1 Not met: no established pathogenic or likely pathogenic variant producing the same p.Leu1111Pro amino-acid change was found.
PS3 Not assessed: no VCEP-approved assay result exists; a 2025 screen reporting normal function is flagged for human review as it is not VCEP-calibrated.
PS4 Not assessed: no case-control study with a qualifying odds ratio or p-value for this variant was available.
PM3 Not assessed: no affected-proband observation or second pathogenic ATM variant in trans was documented.
PP1 Not assessed: no affected relatives, parental testing, or other segregation observations were documented.
PP3 Not met: REVEL 0.644, below the >0.7333 threshold required for missense variants.
Benign
BA1 Not met: grpmax filtering allele frequency 0.000124% (1.24e-06), far below the >0.5% BA1 threshold.
BS1 Not met: grpmax filtering allele frequency 0.000124% (1.24e-06), below the >0.05% BS1 threshold.
BS3 Not assessed: no VCEP-approved assay result exists; a 2025 screen reporting normal function is flagged for human review as it is not VCEP-calibrated.
BP2 Not assessed: no unaffected carrier with a pathogenic ATM variant in trans or phase information was documented.
BP4 Not met: REVEL 0.644 lies above the <=0.249 BP4 threshold (gray zone between BP4 and PP3).
N/A · 16 PVS1 · PS2 · PM1 · PM4 · 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
This variant is present in gnomAD v4.1 (AF= 3.09843e-06; MAF= 0.00031%, 5/1613720 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 4.23788e-06; MAF= 0.00042%, 5/1179836 alleles, homozygotes = 0); grpmax FAF= 1.24e-06.
v2.1
This variant is present in gnomAD v2.1 (AF= 0; MAF= 0.00000%, 0/250754 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/16228 alleles, homozygotes = 0).
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00031% · 5 / 1,613,720
0 hom · FAF 0.00012%
European (non-Finnish)
5 / 1,179,836
0.00042%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
Absent · 0 / 250,754
0 hom
Not observed in any ancestry group.
+ 8 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals, South Asian)
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 (7 clinical laboratories). (ClinVarID = 230062)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.644. BayesDel score = 0.101685.
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 previously been reported in somatic cancers (COSMIC; COSV99592016, n = 1 times).
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 · 7 PMIDs not cited in assessment
25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
40580951 ↗ Functional assessment of all ATM SNVs using prime editing and deep learning. CLINVAR
20301790 ↗ Ataxia-Telangiectasia. CLINVAR
24432435 ↗ PMID 24432435 CLINVAR
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
31429903 ↗ Risk Assessment, Genetic Counseling, and Genetic Testing for BRCA-Related Cancer: US Preventive Services Task Force Recommendation Statement. CLINVAR
35802134 ↗ ACMG SF v3.1 list for reporting of secondary findings in clinical exome and genome sequencing: A policy statement of the American College of Medical Genetics and Genomics (ACMG). CLINVAR