Starting
Initialising…
0%
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
      Population frequency
      Overall AF
      3 / 1,613,944
      0.00019%
      Highest · Remaining individuals
      0.0016%
      Homozygotes
      0
      Allele frequency by ancestry — gnomAD v4.1
      observed in 2 of 9 groups
      AncestryAllele countFrequencyHomozygotes
      South Asian 1 / 91,090 0.0011% 0
      European (non-Finnish) 1 / 1,180,002 8.5e-05% 0
      Admixed American 0 / 60,002
      European (Finnish) 0 / 63,968
      Amish 0 / 912
      East Asian 0 / 44,874
      Middle Eastern 0 / 6,084
      Ashkenazi Jewish 0 / 29,602
      African/African American 0 / 74,930
      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).
      Absent from gnomAD v2.1.
      This variant is absent from gnomAD-Canada.
      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.
      Literature · 13 PMIDs triaged · 8 high-priority
      13papers screened
      Papers triaged by theme: functional/splicing/segregation/case_observation. high_priority_papers include abstract snippets. Use these to support PS3/BS3/PS4/PP1/PP3/PP5.
      25741868 ↗ functional
      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.
      The American College of Medical Genetics and Genomics (ACMG) previously developed guidance for the interpretation of sequence variants.(1) In the past decade, sequencing technology has evolved rapidly with the advent of high-throughput next-generation sequencing. By adopting and leveraging next-generation sequencing, clinical laboratories are now performing an ever-increasing catalogue of genetic
      BS3PP5PS3PS4
      20301317 ↗ case observation
      Untitled reference
      PP5PS4
      20301790 ↗ case observation
      Untitled reference
      PP5PS4
      24418350 ↗ case observation
      EFNS/ENS Consensus on the diagnosis and management of chronic ataxias in adulthood.
      The ataxias are a challenging group of neurological diseases due the aetiological heterogeneity and the complexity of the genetic subtypes. This guideline focuses on the heredodegenerative ataxias. The aim is to provide a peer-reviewed evidence-based guideline for clinical neurologists and other specialist physicians responsible for the care of patients with ataxia. This guideline is based on syst
      PP5PS4
      25394175 ↗ case observation
      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.
      The practice guidelines of the American College of Medical Genetics and Genomics (ACMG) and the National Society of Genetic Counselors (NSGC) are developed by members of the ACMG and NSGC to assist medical geneticists, genetic counselors, and other health-care providers in making decisions about appropriate management of genetic concerns, including access to and/or delivery of services. Each pract
      PP5PS4
      26389210 ↗ case observation
      Untitled reference
      PP5PS4
      26389258 ↗ case observation
      Untitled reference
      PP5PS4
      29939840 ↗ case observation
      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.
      Purpose To update the formal expert consensus-based guideline recommendations for practicing oncologists and others on the management of brain metastases for patients with human epidermal growth factor receptor 2-positive advanced breast cancer to 2018. Methods An Expert Panel conducted a targeted systematic literature review (for both systemic treatment and CNS metastases) and identified 622 arti
      PP5PS4
      20050888 ↗ background review
      EFNS guidelines on the molecular diagnosis of ataxias and spastic paraplegias.
      PP5PS4
      28492532 ↗ background review
      Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
      PP5PS4
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots