Starting
Initialising…
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ATM
Final classification
VUS
ATM c.7381C>T · p.Arg2461Cys
ATM

NM_000051.4:c.7381C>T (p.Arg2461Cys) is a missense variant in ATM, a gene where loss of function is an established mechanism for Ataxia-Telangiectasia (AR) and heterozygous variants confer moderate risk for breast and other cancers (AD).

Gene
ATM
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.7381C>T
Consequence
N/A
GRCh38
chr11:108330287 C>T
GRCh37
chr11:108201014 C>T
Basis Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework was evaluated deterministically with applied criteria: BP4 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: BP4 supporting; no rule matched the adjudicated criteria.
Classification rationale
BP4 VUS
ATM c.7381C>T

NM_000051.4:c.7381C>T (p.Arg2461Cys) is a missense variant in ATM, a gene where loss of function is an established mechanism for Ataxia-Telangiectasia (AR) and heterozygous variants confer moderate risk for breast and other cancers (AD). This variant is not a null variant and SpliceAI predicts no splicing impact (max delta 0.07); PVS1 is not applicable per the ATM VCEP v1.5.0 decision tree.1 This variant is present in gnomAD v4.1 at an overall allele frequency of 0.00613% (99/1,614,160 alleles; 0 homozygotes) with a grpmax filtering AF of 0.039%. The frequency exceeds the PM2_Supporting threshold (≤0.001%) but does not reach BS1 (>0.05%) or BA1 (>0.5%).2 In silico predictions are inconclusive: REVEL score of 0.707 falls between the PP3 threshold (>0.7333) and BP4 missense threshold (≤0.249), neither meeting nor refuting pathogenicity. However, SpliceAI predicts no splicing impact (max delta 0.07 ≤ 0.1), satisfying BP4_Supporting.3 This variant has been reported in ClinVar (VCV000142541) with predominantly uncertain significance classifications (14 clinical laboratories), with a minority of likely benign (3) and benign (1) submissions. No expert panel classification is available.4 Functional evidence from the VCEP-validated Barone 2009 (PMID:19431188) kinase assay suggests partial impairment of ATM autophosphorylation, potentially supporting PS3_Supporting, but full-text verification of the variant-specific result was not possible in this assessment. Human review is recommended.5 No case-control study meeting PS4 criteria, no published segregation data for PP1, and no phased trans/cis data for PM3/BP2 were identified for this variant. Applying the ATM VCEP v1.5.0 criteria combination rules (Richards et al. 2015), only BP4_Supporting is met with no pathogenic criteria satisfied. The variant is classified as a Variant of Uncertain Significance (VUS). If PS3_Supporting is confirmed upon human review of the functional data, the variant would remain VUS (1 pathogenic supporting + 1 benign supporting under Rule31).6

BP4 VUS
1 spliceai ↗vcep_atm_pvs1_1_5
5 vcep_clingen_hbop_atm_supplementary_tables_1_and_2_v1
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= 6.13322e-05; MAF= 0.00613%, 99/1614160 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000519681; MAF= 0.05197%, 39/75046 alleles, homozygotes = 0); grpmax FAF= 0.00038979.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 9.19748e-05; MAF= 0.00920%, 26/282686 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000600625; MAF= 0.06006%, 15/24974 alleles, homozygotes = 0); grpmax FAF= 0.0003336.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0061% · 99 / 1,614,160
      0 hom · FAF 0.039%
      African/African American
      39 / 75,046
      0.052%
      South Asian
      14 / 91,088
      0.015%
      Admixed American
      4 / 60,018
      0.0067%
      European (non-Finnish)
      41 / 1,180,012
      0.0035%
      Remaining individuals
      1 / 62,506
      0.0016%
      + 5 not observed (European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish)
      gnomAD v2.1
      0.0092% · 26 / 282,686
      0 hom · FAF 0.033%
      African/African American
      15 / 24,974
      0.06%
      South Asian
      7 / 30,616
      0.023%
      Remaining individuals
      1 / 7,218
      0.014%
      Admixed American
      1 / 35,436
      0.0028%
      European (non-Finnish)
      2 / 129,028
      0.0016%
      + 3 not observed (Ashkenazi Jewish, East Asian, European (Finnish))
      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 (14 clinical laboratories) and as Likely benign (3 clinical laboratories) and as Benign (1 clinical laboratory) and as Uncertain Significance (1 clinical laboratory). (ClinVarID = 142541)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07). REVEL score = 0.707. BayesDel score = 0.109334.
      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 previously been reported in somatic cancers (COSMIC; COSV53748241, n = 2 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 · 10 PMIDs not cited in assessment
      23532176 ↗ The ATM signaling network in development and disease. CLINVAR
      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
      26010451 ↗ Amplicon sequencing of colorectal cancer: variant calling in frozen and formalin-fixed samples. CLINVAR
      26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. CLINVAR
      27498913 ↗ Monogenic and polygenic determinants of sarcoma risk: an international genetic study. CLINVAR
      27978560 ↗ Prevalence and Spectrum of Germline Cancer Susceptibility Gene Mutations Among Patients With Early-Onset Colorectal Cancer. CLINVAR
      28135145 ↗ Cancer Susceptibility Gene Mutations in Individuals With Colorectal Cancer. CLINVAR
      29058119 ↗ Comprehensive molecular characterisation of epilepsy-associated glioneuronal tumours. 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