Starting
Initialising…
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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 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      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