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 ATM loss-of-function variant is relevant to a DNA-damage-response tumor-suppressor gene in which biallelic loss causes ataxia-telangiectasia and heterozygous loss increases susceptibility to several cancers.
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.8292_8293del
GRCh38
chr11:108343243 AGT>A
GRCh37
chr11:108213970 AGT>A
Pathogenic: PVS1 (very strong) plus PM2 and PM5 (supporting) satisfy ATM VCEP v1.5 Rule4.
Classification rationale
PVS1PM2PM5Pathogenic
ATM c.8292_8293delframeshift · exon 57
Pathogenic: the ATM frameshift meets the VCEP's very-strong PVS1 truncation rule. Pathogenic evidence: PM2 supporting is met by the very low gnomAD v4.1 frequency. Pathogenic evidence: PM5 supporting is met because termination occurs upstream of the ATM p.Arg3047 cutoff.
PVS1 + PM2 + PM5→Pathogenic
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Gene diagram
· NM_000051.4 · variants mapped to exon structure
ATMNM_000051.4
Fetching transcript structure from UCSC…
Exons
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Transcript span
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Strand
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Variants mapped
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Source
UCSC ncbiRefSeqCurated
All variants in ATM—click a row to locate it on the plot · use the link column to open its page
Protein
Location
Classification
Link
Applied criteria · 3 applied · 8 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 · 3
Strength Supporting Moderate Strong Very strong
✓
PVS1very strongPathogenic
Met, very strong: the frameshift terminates at approximately p.2767, upstream of ATM's p.Arg3047 pathogenic truncation boundary.
The case normalization identifies NM_000051.4:c.8292_8293del as a frameshift encoding NP_000042.3:p.(Ser2764ArgfsTer4) / p.(S2764Rfs*4).ATM HBOP VCEP v1.5 PVS1 defines frameshift variants as null variants when loss of function is a known disease mechanism, specifies NM_000051.3/ENST00000278616.8 as the default transcript, and considers all exons in that transcript constitutive without major rescue isoforms.ATM HBOP VCEP v1.5 identifies p.Arg3047 as the most 3-prime/C-terminal residue considered pathogenic; the predicted stop near p.2767 is upstream of that boundary.
Met at supporting: gnomAD v4.1 total AF is 1.858874e-6 (0.0001859%), below the ATM VCEP PM2 threshold of <=0.001%.
ATM VCEP v1.5 PM2 rule: use PM2 Supporting for frequency <=0.001% in gnomAD v4.1; one allele in a single subpopulation is sufficient.gnomAD v4.1 reports total AF 1.858874e-6 (0.0001859%; 3/1,613,880 alleles), grpmax FAF 6.8e-7, highest observed subpopulation AF 2.542515e-6 in European (non-Finnish) individuals, and homozygotes = 0.The ATM VCEP specifies gnomAD v4.1 without a non-cancer or exome-only restriction for PM2, so the combined all-comers gnomAD v4.1 values are used.
Met, supporting: p.(Ser2764ArgfsTer4) is a frameshift termination upstream of the ATM VCEP PM5 cutoff at p.Arg3047.
The ClinGen HBOP ATM VCEP v1.5 PM5 rule states: apply to frameshifting or truncating variants with premature termination codons upstream of p.Arg3047, with Supporting strength specified.The variant is NM_000051.4:c.8292_8293del, producing NP_000042.3:p.(Ser2764ArgfsTer4), a premature termination far upstream of p.Arg3047.
Assessed · not applied
· 2 not met · 6 not assessed
Pathogenic
PS3Not assessed: no qualifying ATM-specific assay result was documented for c.8292_8293del, so the VCEP PS3 strength thresholds cannot be applied.
PS4Not assessed: no qualifying case-control p-value, odds ratio, hazard ratio, relative risk, or lower 95% confidence interval was available for this exact variant.
PM3Not assessed: no affected-proband observation documents this variant with a second ATM pathogenic variant in trans or qualifying homozygosity for PM3 points.
PP1Not assessed: zero affected-relative segregations are documented, versus the ATM VCEP threshold of one affected relative for PP1 supporting.
Benign
BA1Not met: gnomAD v4.1 grpmax FAF is 6.8e-7 (0.000068%), below the ATM VCEP BA1 threshold of >0.5%.
BS1Not met: gnomAD v4.1 grpmax FAF is 6.8e-7 (0.000068%), below the ATM VCEP BS1 threshold of >0.05%.
BS3Not assessed: no variant-specific rescue of ATM function or radiosensitivity was documented, so the VCEP BS3 thresholds cannot be applied.
BP2Not assessed: no unaffected adult carrying this variant with a pathogenic ATM variant in trans or qualifying homozygosity is documented.
This variant is present in gnomAD v4.1 (AF= 1.85887e-06; MAF= 0.00019%, 3/1613880 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.54252e-06; MAF= 0.00025%, 3/1179934 alleles, homozygotes = 0); grpmax FAF= 6.8e-07.
v2.1
This variant is present in gnomAD v2.1 (AF= 7.07304e-06; MAF= 0.00071%, 2/282764 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.54904e-05; MAF= 0.00155%, 2/129112 alleles, homozygotes = 0).
🇨🇦 CA
Not available in gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00019%
· 3 / 1,613,880
0 hom · FAF 6.8e-05%
European (non-Finnish)
3 / 1,179,934
0.00025%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.00071%
· 2 / 282,764
0 hom
European (non-Finnish)
2 / 129,112
0.0015%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
This variant has been reported in ClinVar as Pathogenic (7 clinical laboratories) and as Likely pathogenic (1 clinical laboratory). (ClinVarID = 245989)
Triaged references · 8 PMIDs not cited in assessment
27413114 ↗ATM Mutations in Cancer: Therapeutic Implications.ONCOKB
30348496 ↗Inactive Atm abrogates DSB repair in mouse cerebellum more than does Atm loss, without causing a neurological phenotype.ONCOKB
30553448 ↗Loss of ATM positively regulates Rac1 activity and cellular migration through oxidative stress.ONCOKB
23807571 ↗Twelve novel Atm mutations identified in Chinese ataxia telangiectasia patients.CLINVAR
25614872 ↗Ten new ATM alterations in Polish patients with ataxia-telangiectasia.CLINVAR
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
31050087 ↗Functional classification of ATM variants in ataxia-telangiectasia patients.CLINVAR
34242744 ↗Customizing local and systemic therapies for women with early breast cancer: the St. Gallen International Consensus Guidelines for treatment of early breast cancer 2021.CLINVAR