Starting
Initialising…
0%
ATM
Final classification
Uncertain Significance - Conflicting Evidence
ATM c.7486G>C · p.Gly2496Arg
ATM

NM_000051.4:c.7486G>C (p.Gly2496Arg) is a missense variant in ATM exon 50.

Gene
ATM
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.7486G>C
Consequence
N/A
GRCh38
chr11:108330392 G>C
GRCh37
chr11:108201119 G>C
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; 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; maps to Uncertain Significance - Conflicting Evidence.
Classification rationale
PM2 BP4 Uncertain Significance - Conflicting Evidence
ATM c.7486G>C

NM_000051.4:c.7486G>C (p.Gly2496Arg) is a missense variant in ATM exon 50. This variant is extremely rare in population databases: present in gnomAD v4.1 at an allele frequency of 0.00037% (6/1,614,098 alleles, 0 homozygotes), meeting the VCEP threshold for PM2_Supporting.1 Multiple lines of computational evidence suggest a benign effect: REVEL score is 0.189 (meeting the VCEP BP4 threshold of ≤0.249), BayesDel score is negative (-0.183511), and SpliceAI predicts no splicing impact (max delta 0.04). BP4_Supporting is applied.2 The ATM VCEP supplementary in silico meta-predictor (Suppl_TableS1, PMID:40580951) classifies this variant as 'Functional' with High confidence (Combined score 0.962), consistent with the benign computational evidence.3 This variant has been reported in ClinVar as Uncertain significance by three clinical laboratories (Variation ID: 569749).4 PVS1, PS1, PM1, PM5, PM6, PS2, PP1, PP2, PP4, PP5, BS2, BS4, BP1, BP5, BP6, and BP7 are not applicable per ATM VCEP v1.5.0 specifications.5 No variant-specific experimental functional studies, case-control data, or segregation data were identified for this variant. Applying the ATM VCEP v1.5.0 classification framework: PM2_Supporting (1 pathogenic supporting point) and BP4_Supporting (1 benign supporting point). Per the generic ACMG/AMP 2015 combination rules (Rule 31), one pathogenic supporting criterion and one benign supporting criterion result in conflicting evidence, yielding an overall classification of Uncertain Significance.6

PM2 + BP4 Uncertain Significance - Conflicting Evidence
2 revelbayesdelspliceai ↗
3 vcep_suppl_tables1_pmid_40580951
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= 3.71725e-06; MAF= 0.00037%, 6/1614098 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 5.08477e-06; MAF= 0.00051%, 6/1179994 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 / 1,614,098
      0 hom · FAF 0.00018%
      European (non-Finnish)
      6 / 1,179,994
      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 = 569749)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04). REVEL score = 0.189. BayesDel score = -0.183511.
      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
      9Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 5 PMIDs not cited in assessment
      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
      20050888 ↗ EFNS guidelines on the molecular diagnosis of ataxias and spastic paraplegias. CLINVAR