Starting
Initialising…
0%
ATM
Final classification
Uncertain Significance - Conflicting Evidence
ATM c.8047A>G · p.Ile2683Val
ATM

This variant is a missense substitution (c.8047A>G, p.Ile2683Val) in ATM, assessed under the ClinGen HBOP VCEP v1.5.0 framework.

Gene
ATM
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.8047A>G
Consequence
N/A
GRCh38
chr11:108335005 A>G
GRCh37
chr11:108205732 A>G
Basis Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework: matched Rule31 (Benign.Supporting >=1 + Pathogenic.Supporting >=1) with applied criteria: PM2 supporting, BP4 supporting benign; maps to Uncertain Significance - Conflicting Evidence.
Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework: matched Rule31 (Benign.Supporting >=1 + Pathogenic.Supporting >=1) with applied criteria: PM2 supporting, BP4 supporting benign; maps to Uncertain Significance - Conflicting Evidence.
Classification rationale
PM2 BP4 Uncertain Significance - Conflicting Evidence
ATM c.8047A>G

This variant is a missense substitution (c.8047A>G, p.Ile2683Val) in ATM, assessed under the ClinGen HBOP VCEP v1.5.0 framework.1 The variant is present in gnomAD v4.1 at a very low frequency (AF=0.00081%, 13/1,613,486 alleles, grpmax FAF=0.0005%), meeting the PM2_Supporting criterion (≤0.001% threshold).2 Computational evidence supports a benign effect: REVEL score of 0.165 (≤0.249 threshold), BayesDel score of -0.311657, and SpliceAI predicts no splicing impact (max delta=0.00, ≤0.1), meeting BP4_Supporting. The VCEP supplementary computational meta-predictor (Suppl_TableS1, PMID 40580951) classifies this variant as Functional with High confidence.3 No functional assay data (kinase activity or radiosensitivity rescue) are available for this variant, so PS3 and BS3 cannot be assessed.4 No case-control studies, segregation data, or trans/homozygous observations in unaffected individuals were identified, leaving PS4, PP1, and BP2 unassessed.5 ClinVar lists this variant as Uncertain significance (3 clinical laboratories) and Likely benign (1 clinical laboratory) with no expert panel submissions.6 Applying the VCEP combining rules: PM2_Supporting (1 pathogenic supporting) and BP4_Supporting (1 benign supporting) yields a classification of Uncertain Significance - Conflicting Evidence per Rule 31.7

PM2 + BP4 Uncertain Significance - Conflicting Evidence
3 revelspliceai ↗bayesdelvcep_suppl_tables1_pmid_40580951cspec ↗
4 vcep_clingen_hbop_atm_supplementary_tables_1_and_2_v1cspec ↗
7 final_classification_frameworkcspec ↗
Gene diagram · NM_000051.4 · variants mapped to exon structure
ATM NM_000051.4
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= 8.05709e-06; MAF= 0.00081%, 13/1613486 alleles, homozygotes = 0) and has highest observed frequency in the Middle Eastern population (AF= 0.000165017; MAF= 0.01650%, 1/6060 alleles, homozygotes = 0); grpmax FAF= 5e-06.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 7.95944e-06; MAF= 0.00080%, 2/251274 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.76047e-05; MAF= 0.00176%, 2/113606 alleles, homozygotes = 0); grpmax FAF= 2.92e-06.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00081% · 13 / 1,613,486
      0 hom · FAF 0.0005%
      Middle Eastern
      1 / 6,060
      0.017%
      Remaining individuals
      1 / 62,484
      0.0016%
      European (non-Finnish)
      11 / 1,179,428
      0.00093%
      + 7 not observed (Admixed American, European (Finnish), Amish, East Asian, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0008% · 2 / 251,274
      0 hom · FAF 0.00029%
      European (non-Finnish)
      2 / 113,606
      0.0018%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (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 (3 clinical laboratories) and as Likely benign (1 clinical laboratory). (ClinVarID = 453719)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.165. BayesDel score = -0.311657.
      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.
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 10 PMIDs not cited in assessment
      28779002 ↗ Rare, protein-truncating variants in ATM, CHEK2 and PALB2, but not XRCC2, are associated with increased breast cancer risks. 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
      26389210 ↗ Genetics of Breast and Gynecologic Cancers (PDQ®): Health Professional Version. CLINVAR
      26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version. CLINVAR
      29939840 ↗ Recommendations on Disease Management for Patients With Advanced Human Epidermal Growth Factor Receptor 2-Positive Breast Cancer and Brain Metastases: ASCO Clinical Practice Guideline Update. CLINVAR
      20050888 ↗ EFNS guidelines on the molecular diagnosis of ataxias and spastic paraplegias. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR