Starting
Initialising…
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ATM
Final classification
Uncertain Significance - Conflicting Evidence
ATM c.5600A>G · p.Gln1867Arg
ATM

NM_000051.4:c.5600A>G (p.Gln1867Arg) is a missense variant in exon 37 of ATM. It has been reported in ClinVar as a variant of uncertain significance (ClinVar ID 453589, 4 clinical laboratories).

Gene
ATM
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.5600A>G
Consequence
N/A
GRCh38
chr11:108304778 A>G
GRCh37
chr11:108175505 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: PS3 supporting, PM2 supporting, BP4 supporting; 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: PS3 supporting, PM2 supporting, BP4 supporting; maps to Uncertain Significance - Conflicting Evidence.
Classification rationale
PS3PM2 BP4 Uncertain Significance - Conflicting Evidence
ATM c.5600A>G

NM_000051.4:c.5600A>G (p.Gln1867Arg) is a missense variant in exon 37 of ATM. It has been reported in ClinVar as a variant of uncertain significance (ClinVar ID 453589, 4 clinical laboratories).1 This variant is present in gnomAD v4.1 at an extremely low allele frequency (AF = 1.86e-6, 3/1,613,944 alleles, 0 homozygotes) and is absent from gnomAD v2.1 and gnomAD-Canada, meeting the ATM VCEP PM2_Supporting threshold (≤0.001%).2 The ATM VCEP supplementary functional data (Suppl_TableS1, PMID 40580951) classifies this variant as 'Non-functional' (combined score -2.05, Medium-high confidence), meeting PS3_Supporting per the VCEP framework for variants that fail to rescue ATM-specific functional features.3 Multiple computational predictors suggest a benign effect: REVEL score 0.088 (meeting BP4_Supporting threshold ≤0.249), BayesDel -0.34033, AlphaMissense 0.0758. SpliceAI predicts no splicing impact (max delta 0.10, meeting BP4 splicing threshold ≤0.1).4 No case-control studies, co-segregation data, or confirmed de novo observations have been identified for this variant. A ClinVar submission noting observation in trans with a pathogenic ATM variant in an A-T patient was not accompanied by peer-reviewed publication, precluding application of PM3.5 The variant has not been reported in COSMIC and is not located in a statistically significant cancer hotspot residue.

PS3 + PM2 + BP4 Uncertain Significance - Conflicting Evidence
3 vcep_suppl_tables1_pmid_40580951
4 revelbayesdelspliceai ↗
Gene diagram · NM_000051.4 · variants mapped to exon structure
ATM NM_000051.4
Fetching transcript structure from UCSC…
Applied criteria · 3 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= 1.8588e-06; MAF= 0.00019%, 3/1613944 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 1.60051e-05; MAF= 0.00160%, 1/62480 alleles, homozygotes = 0).
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00019% · 3 / 1,613,944
      0 hom
      Remaining individuals
      1 / 62,480
      0.0016%
      South Asian
      1 / 91,090
      0.0011%
      European (non-Finnish)
      1 / 1,180,002
      8.5e-05%
      + 7 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, 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 (4 clinical laboratories). (ClinVarID = 453589)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.10). REVEL score = 0.088. BayesDel score = -0.34033.
      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
      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
      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