Starting
Initialising…
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ATM
Final classification
VUS
ATM c.8261C>T · p.Thr2754Ile
ATM

NM_000051.4:c.8261C>T (p.Thr2754Ile) is a missense variant in ATM, a gene for which loss of function is an established mechanism of disease in ataxia-telangiectasia and in which germline variants confer susceptibility to breast, ovarian, and pancreatic cancer (ClinGen HBOP VCEP v1.5.0).

Gene
ATM
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.8261C>T
Consequence
N/A
GRCh38
chr11:108335954 C>T
GRCh37
chr11:108206681 C>T
Basis Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting; no rule matched the adjudicated criteria.
Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting; no rule matched the adjudicated criteria.
Classification rationale
PM2 VUS
ATM c.8261C>T

NM_000051.4:c.8261C>T (p.Thr2754Ile) is a missense variant in ATM, a gene for which loss of function is an established mechanism of disease in ataxia-telangiectasia and in which germline variants confer susceptibility to breast, ovarian, and pancreatic cancer (ClinGen HBOP VCEP v1.5.0).1 This variant is present at extremely low frequency in population databases: gnomAD v4.1 reports 4 heterozygous carriers among 1,605,254 alleles (total AF=2.49e-06; grpmax FAF=2.8e-07) with no homozygotes observed, and gnomAD v2.1 reports 1 heterozygous carrier among 31,352 alleles (AF=3.19e-05). It is absent from gnomAD-Canada v1.0.2 In silico predictors are inconclusive: REVEL score is 0.633 (below the ATM VCEP PP3 threshold of >0.7333 but above the BP4 threshold of ≤0.249), BayesDel score is -0.0763065, and SpliceAI predicts no significant splice impact (max delta score = 0.01).3 This variant has been reported in ClinVar as Uncertain Significance by 6 clinical laboratories (ClinVar Variation ID: 127457), with no expert panel classifications available. No functional studies, case-control analyses, segregation data, or observations in trans with pathogenic ATM variants have been identified for this specific variant.4 The variant is absent from COSMIC (no somatic cancer reports) and does not fall within a statistically significant Cancer Hotspot. OncoKB reports no reviewed functional evidence and classifies this variant as having Unknown Oncogenic Effect.5 Under the ClinGen HBOP VCEP for ATM v1.5.0, only PM2_Supporting is met (allele frequency ≤0.001% in gnomAD v4). All other applicable criteria are either not met or not applicable. With a single supporting-level pathogenic criterion and no benign criteria met, the variant is classified as Uncertain Significance (VUS) per the ACMG/AMP 2015 combining rules as adopted by the ATM VCEP.6

PM2 VUS
Gene diagram · NM_000051.4 · variants mapped to exon structure
ATM NM_000051.4
Fetching transcript structure from UCSC…
Applied criteria · 1 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= 2.49182e-06; MAF= 0.00025%, 4/1605254 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 2.23085e-05; MAF= 0.00223%, 1/44826 alleles, homozygotes = 0); grpmax FAF= 2.8e-07.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 3.18959e-05; MAF= 0.00319%, 1/31352 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 6.48677e-05; MAF= 0.00649%, 1/15416 alleles, homozygotes = 0).
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00025% · 4 / 1,605,254
      0 hom · FAF 2.8e-05%
      East Asian
      1 / 44,826
      0.0022%
      African/African American
      1 / 74,682
      0.0013%
      European (non-Finnish)
      2 / 1,172,242
      0.00017%
      + 7 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, Middle Eastern, South Asian, Ashkenazi Jewish)
      gnomAD v2.1
      0.0032% · 1 / 31,352
      0 hom
      European (non-Finnish)
      1 / 15,416
      0.0065%
      + 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 (6 clinical laboratories). (ClinVarID = 127457)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.633. BayesDel score = -0.0763065.
      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 · 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
      27978560 ↗ Prevalence and Spectrum of Germline Cancer Susceptibility Gene Mutations Among Patients With Early-Onset Colorectal Cancer. CLINVAR
      34242744 ↗ Customizing local and systemic therapies for women with early breast cancer: the St. Gallen International Consensus Guidelines for treatment of early breast cancer 2021. CLINVAR
      15604628 ↗ Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors. CLINVAR
      17508274 ↗ Risk assessment and genetic counseling for hereditary breast and ovarian cancer: recommendations of the National Society of Genetic Counselors. CLINVAR
      18163131 ↗ The emerging landscape of breast cancer susceptibility. CLINVAR
      20301317 ↗ PMID:20301317 CLINVAR
      20301425 ↗ BRCA1- and BRCA2-Associated Hereditary Breast and Ovarian Cancer. 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