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NM_000051.4:c.182T>G
p.Phe61Cys · ATM
0%
complete
Final classification
Uncertain Significance - Conflicting Evidence
PM2BS3
ATM
c.182T>G
p.Phe61Cys
missense · exon 3

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

For ATM, the governing Version 1.6 framework excludes PS2, PM6, and BS4; PP1 is potentially applicable but requires documented affected-relative segregation that is absent from the available case evidence.

Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.182T>G
GRCh38
chr11:108227885 T>G
GRCh37
chr11:108098612 T>G
ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for ATM Version 1.6 v1.6 criteria-combination framework: matched Rule31 (Benign.Supporting >=1 + Pathogenic.Supporting >=1) with applied criteria: PM2 supporting, BS3 supporting; maps to Uncertain Significance - Conflicting Evidence.
Classification rationale
PM2 BS3 Uncertain Significance - Conflicting Evidence
ATM c.182T>G missense · exon 3

For ATM, the governing Version 1.6 framework excludes PS2, PM6, and BS4; PP1 is potentially applicable but requires documented affected-relative segregation that is absent from the available case evidence. The exact Table S1 entry is direct functional measurement (DeepATM_predicted=No) and is classified Functional with Medium-high confidence, supporting benign functional evidence rather than pathogenic functional loss. The ATM VCEP-approved calibration file was searched under c.182T>G, p.Phe61Cys, and p.F61C; it contains no variant-specific entry and only calibrates three approved kinase assays and the approved Mitui radiosensitivity assay. BS3 Supporting is recorded provisionally with needs_human_review=true because the direct prime-editing assay is outside the current approved assay set; PS3 is not met because the result is Functional rather than non-functional. The ClinGen HBOP ATM VCEP version 1.6 governs this assessment. PS4 remains not assessed because variant-specific case-control enrichment statistics are absent. PP4, PP5, BP5, and BP6 are excluded or not applicable under the ATM VCEP; no expert-panel ClinVar assertion is present. The variant is missense, so PP3 and BP4 use REVEL only; REVEL 0.62 meets neither the ATM VCEP PP3 threshold (>0.7333) nor the BP4 threshold (<=0.249). BP7 is not applicable because the variant is not synonymous or qualifying deep-intronic. Population evidence supports PM2 at supporting strength because the variant is absent from gnomAD v2.1 and v4.1. BA1 and BS1 are not met because the variant is not observed at their ATM VCEP frequency thresholds. BS2 is not applicable under the ATM VCEP because ATM-related cancer predisposition has incomplete penetrance.

PM2 + BS3 → Uncertain Significance - Conflicting Evidence
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 · 2 applied · 10 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 · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
Met at supporting strength: the variant is absent from gnomAD v2.1 and v4.1, satisfying the ATM PM2 threshold of ≤0.001%.
ClinGen HBOP ATM VCEP version 1.6 specifies PM2 at supporting strength for frequency ≤0.001% in the highest-frequency gnomAD subpopulation.The variant is absent from gnomAD v2.1 and gnomAD v4.1, giving an observed frequency of zero in the available default population datasets.
BS3 supporting review Benign
Met, provisionally: direct prime-editing classified c.182T>G as Functional with Medium-high confidence, consistent with retained ATM function and BS3 Supporting.
The exact variant row in Table S1 is chr11:108227885 T>G, c.182T>G, F61C, Missense, with Classification Functional, Confidence Medium-high, and DeepATM_predicted No.The direct-measurement flag DeepATM_predicted=No distinguishes this row from computational extrapolations and supports treating it as direct functional evidence.The ATM VCEP BS3 rule assigns Supporting when a variant rescues either an ATM-specific feature or radiosensitivity, and Moderate when it rescues both.
Assessed · not applied · 5 not met · 5 not assessed
Pathogenic
PS1 Not assessed: no established p.Phe61Cys comparator was identified, and SpliceAI returned no score to rule out a splice defect.
PS3 Not met: Table S1 directly measured c.182T>G as Functional, not a failure of ATM function, but the assay is outside the VCEP-approved assay set.
PS4 Not assessed: no case-control p-value, odds ratio, relative risk, hazard ratio, or lower 95% confidence interval is available for this variant.
PM3 Not assessed: no affected Ataxia-Telangiectasia proband or qualifying pathogenic allele in trans was documented, so the VCEP PM3 point total is unavailable.
PP1 Not assessed: no affected-relative segregation, parental testing, pedigree, or meiosis data are documented for this variant.
PP3 Not met: REVEL 0.62 is below the ATM VCEP PP3 Supporting threshold of >0.7333 for missense variants.
Benign
BA1 Not met: the variant is absent from gnomAD v2.1 and v4.1, rather than exceeding the ATM VCEP BA1 threshold of >0.5%.
BS1 Not met: the variant is absent from gnomAD v2.1 and v4.1, rather than exceeding the ATM VCEP BS1 threshold of >0.05%.
BP2 Not assessed: no unaffected adult carrying the variant with a qualifying pathogenic ATM allele in trans was documented, so the VCEP BP2 point total is unavailable.
BP4 Not met: REVEL 0.62 exceeds the ATM VCEP BP4 Supporting threshold of <=0.249 for missense variants.
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
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 is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI returned NO scores for this variant, so no SpliceAI-based splice prediction is available. This is missing data, NOT evidence of absent splice impact: it must not be used to support BP4 or to argue against PP3/PVS1. Pangolin scores may be present but are not calibrated for PP3/BP4 here. REVEL score = 0.62. BayesDel score = 0.219157.
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.
Literature · how each cited paper was used
1papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why.
PMID 40580951
Found
Structured finding pending for this record — see source link.
Applied to
→BS3 supporting
Direct Functional classification supports retained ATM function and provisional BS3 Supporting.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots