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ATM
Final classification
VUS
ATM c.8174A>G · p.Asp2725Gly
ATM

NM_000051.3:c.8174A>G (p.Asp2725Gly) in ATM is a rare missense variant observed in gnomAD v4.1 at a frequency of 0.00037% (6/1,613,960 alleles), meeting ATM VCEP PM2_Supporting.

Gene
ATM
Transcript
NM_000051.3
HGVS · transcript:coding
NM_000051.3:c.8174A>G
Consequence
N/A
GRCh38
chr11:108335867 A>G
GRCh37
chr11:108206594 A>G
Basis Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting, PP3 supporting; no rule matched the adjudicated criteria.
Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting, PP3 supporting; no rule matched the adjudicated criteria.
Classification rationale
PM2PP3 VUS
ATM c.8174A>G

NM_000051.3:c.8174A>G (p.Asp2725Gly) in ATM is a rare missense variant observed in gnomAD v4.1 at a frequency of 0.00037% (6/1,613,960 alleles), meeting ATM VCEP PM2_Supporting.1 In silico prediction tools consistently suggest a deleterious effect: REVEL score of 0.968 exceeds the ATM VCEP PP3_Supporting threshold of >0.7333, and the ClinGen HBOP VCEP supplemental table classifies this variant as Non-functional with Medium-high confidence based on combined computational scores.2 No functional studies, segregation data, case-control analyses, or trans-observation data are available for this variant. The variant has not been reported as pathogenic by any reputable source.3 With PM2_Supporting and PP3_Supporting as the only met criteria, this variant does not reach the threshold for Likely Pathogenic or Likely Benign under the ClinGen HBOP VCEP v1.5.0 combination rules. The classification is Uncertain Significance.4

PM2 + PP3 VUS
2 revelvcep_suppl_tables1_pmid_40580951
Gene diagram · NM_000051.3 · variants mapped to exon structure
ATM NM_000051.3
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 10 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
The variant frequency in gnomAD v4.1 (AF=0.00037%, 6/1,613,960 alleles; grpmax FAF=0.00018%) is ≤0.001% per the ATM VCEP PM2 rule. The variant is absent from gnomAD v2.1 and gnomAD-Canada. At 0.00037%, this meets the VCEP PM2_Supporting threshold.
gnomAD v4.1: 6/1613960 alleles
PP3 supporting Pathogenic
REVEL score of 0.968 exceeds the ATM VCEP PP3 threshold of >0.7333 for missense variants. SpliceAI predicts no significant splice impact (max delta=0.07). The VCEP supplemental table (PMID:40580951) independently classifies this variant as Non-functional based on a combined computational score integrating boostDM, EVE, REVEL, and AlphaMissense, consistent with a deleterious in silico prediction.
REVEL=0.968 (>0.7333 threshold)SpliceAI max_delta=0.07 (no splicing concern)VCEP supplement table classifies variant as Non-functional (Medium-high confidence) based on combined computational scores.
Assessed · not applied
Pathogenic
PS1 No known pathogenic or likely pathogenic variant has been established at the same nucleotide position (c.8174).
PS3 No variant-specific functional assay data have been reported for NM_000051.3:c.8174A>G.
PS4 No case-control study has been identified that provides variant-specific odds ratio, relative risk, or p-value for NM_000051.3:c.8174A>G.
PP1 No segregation data are available for NM_000051.3:c.8174A>G.
PP5 No reputable source has reported NM_000051.3:c.8174A>G as pathogenic.
Benign
BA1 The grpmax filtering allele frequency in gnomAD v4.1 is 0.00018% (FAF=1.83e-06), which is well below the ATM VCEP BA1 threshold of >0.5%.
BS1 The grpmax filtering allele frequency in gnomAD v4.1 is 0.00018% (FAF=1.83e-06), which is below the ATM VCEP BS1 threshold of >0.05%.
BS3 No experimental functional studies demonstrating rescue of ATM function have been reported for NM_000051.3:c.8174A>G.
BP2 No observations of NM_000051.3:c.8174A>G in trans with a pathogenic ATM variant in an unaffected individual were identified.
BP4 REVEL score of 0.968 exceeds the ATM VCEP BP4 missense threshold of ≤0.249.
N/A · 13 PVS1 · PS2 · PM1 · PM5 · PM6 · PP2 · PP4 · BS2 · BS4 · BP1 · 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= 3.71756e-06; MAF= 0.00037%, 6/1613960 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 5.08521e-06; MAF= 0.00051%, 6/1179892 alleles, homozygotes = 0); grpmax FAF= 1.83e-06.
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
0.00037% · 6 / 1,613,960
0 hom · FAF 0.00018%
European (non-Finnish)
6 / 1,179,892
0.00051%
+ 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 / ?
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 (3 clinical laboratories). (ClinVarID = 482631)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07). REVEL score = 0.968. BayesDel score = 0.482249.
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; COSV53728899, n = 3 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 · 9 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
28779002 ↗ Rare, protein-truncating variants in ATM, CHEK2 and PALB2, but not XRCC2, are associated with increased breast cancer risks. CLINVAR
9334731 ↗ Biallelic mutations in the ATM gene in T-prolymphocytic leukemia. CLINVAR
20301317 ↗ Hereditary Ataxia Overview. CLINVAR
20301790 ↗ Ataxia-Telangiectasia. CLINVAR
24418350 ↗ EFNS/ENS Consensus on the diagnosis and management of chronic ataxias in adulthood. 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
33471991 ↗ Breast Cancer Risk Genes - Association Analysis in More than 113,000 Women. CLINVAR
20050888 ↗ EFNS guidelines on the molecular diagnosis of ataxias and spastic paraplegias. CLINVAR