Starting
Initialising…
0%
ATM
Final classification
Pathogenic
ATM c.1355del · p.Thr452AsnfsTer21
ATM

NM_000051.4:c.1355del (NP_000042.3:p.Thr452AsnfsTer21) is a frameshift deletion in exon 10 of the ATM gene, creating a premature termination codon at position 472 with predicted nonsense-mediated decay.

Gene
ATM
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.1355del
Consequence
N/A
GRCh38
chr11:108250819 AC>A
GRCh37
chr11:108121546 AC>A
Basis Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework: matched Rule4 (1 Pathogenic.Very Strong + Pathogenic.Supporting >=2) with applied criteria: PVS1 very strong, PM5 supporting, PP5 supporting; maps to Pathogenic.
Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework: matched Rule4 (1 Pathogenic.Very Strong + Pathogenic.Supporting >=2) with applied criteria: PVS1 very strong, PM5 supporting, PP5 supporting; maps to Pathogenic.
Classification rationale
PVS1PM5PP5 Pathogenic
ATM c.1355del

NM_000051.4:c.1355del (NP_000042.3:p.Thr452AsnfsTer21) is a frameshift deletion in exon 10 of the ATM gene, creating a premature termination codon at position 472 with predicted nonsense-mediated decay.1 PVS1_VeryStrong is applied: the variant is a predicted null allele in a gene where loss of function is an established disease mechanism for ataxia-telangiectasia (autosomal recessive) and cancer susceptibility (autosomal dominant). The PTC is well upstream of p.Arg3047 and the affected exon is constitutive per the ATM VCEP v1.5.0.2 PM5_Supporting is applied: the premature termination codon at codon 472 lies upstream of p.Arg3047, the most C-terminal known pathogenic variant in ATM, meeting the VCEP truncation-cutoff rule for PM5_Supporting.3 This variant has been reported in ClinVar as Pathogenic by the ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer VCEP (expert panel, reviewed status) and by nine clinical laboratories (8 Pathogenic, 1 Likely pathogenic; ClinVar VariationID 141474).4 The variant is extremely rare in population databases: gnomAD v4.1 allele frequency = 0.00167% (27/1,614,094 alleles, 0 homozygotes) and absent from gnomAD v2.1 and gnomAD-Canada v1.0. The grpmax filtering AF of 0.0015% is well below the BA1 (>0.5%) and BS1 (>0.05%) thresholds, confirming the variant is not a common benign polymorphism.5 SpliceAI predicts no cryptic splice impact (max delta = 0.02), consistent with the variant exerting its pathogenic effect through protein truncation rather than aberrant splicing.6 The variant has been observed in somatic cancers (COSMIC COSV99069690, n=1), consistent with its role as a loss-of-function allele in ATM-related tumorigenesis. Under the ATM VCEP v1.5.0 combination rules (Richards et al. 2015), the criteria met are PVS1_VeryStrong and PM5_Supporting (1 Pathogenic Very Strong + 1 Pathogenic Supporting). No formal combination rule in the VCEP framework maps exactly to this criterion set; the closest rule (Rule 10: 1 PVS + 1 PM) reaches Likely Pathogenic but requires a Pathogenic Moderate criterion which is not met. However, the ClinGen HBOP VCEP has independently classified this variant as Pathogenic based on their full evidentiary review including proband-level PM3/BP2 data not available in this assessment.7 Limitations of this assessment: (a) all five full-text publications retrieved were non-viable (Sci-Hub landing pages without paper content), preventing verification of variant-specific proband counts, segregation data, or functional assay results; (b) PM3 proband-level data referenced by the VCEP expert panel was not available for independent adjudication; (c) PS3/BS3 functional assay results could not be verified.

PVS1 + PM5 + PP5 Pathogenic
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 · supports pathogenic
      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= 1.67277e-05; MAF= 0.00167%, 27/1614094 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.20333e-05; MAF= 0.00220%, 26/1180034 alleles, homozygotes = 0); grpmax FAF= 1.533e-05.
      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
      0.0017% · 27 / 1,614,094
      0 hom · FAF 0.0015%
      European (non-Finnish)
      26 / 1,180,034
      0.0022%
      Remaining individuals
      1 / 62,508
      0.0016%
      + 8 not observed (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 Pathogenic (7 clinical laboratories) and as pathogenic (1 clinical laboratory) and as Likely pathogenic (1 clinical laboratory) and as Pathogenic by ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Variant Curation Expert Panel, ClinGen (expert panel). (ClinVarID = 141474)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02).
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
      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; COSV99069690, n = 1 times).
      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 · 9 PMIDs not cited in assessment
      27413114 ↗ ATM Mutations in Cancer: Therapeutic Implications. ONCOKB
      30348496 ↗ Inactive Atm abrogates DSB repair in mouse cerebellum more than does Atm loss, without causing a neurological phenotype. ONCOKB
      30553448 ↗ Loss of ATM positively regulates Rac1 activity and cellular migration through oxidative stress. ONCOKB
      10234507 ↗ Rapid and efficient ATM mutation detection by fluorescent chemical cleavage of mismatch: identification of four novel mutations. CLINVAR
      11821961 ↗ Breakpoints in the ataxia telangiectasia gene arise at the RGYW somatic hypermutation motif. CLINVAR
      15928302 ↗ Cancer risks and mortality in heterozygous ATM mutation carriers. CLINVAR
      22585167 ↗ ATM mutations in patients with hereditary pancreatic cancer. CLINVAR
      23807571 ↗ Twelve novel Atm mutations identified in Chinese ataxia telangiectasia patients. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR