Starting
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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
      Population frequency
      Overall AF
      99 / 1,614,160
      0.0061%
      Highest · African/African American
      0.052%
      Homozygotes
      0
      grpmax FAF
      0.039%
      Allele frequency by ancestry — gnomAD v4.1
      observed in 4 of 9 groups
      AncestryAllele countFrequencyHomozygotes
      African/African American 39 / 75,046 0.052% 0
      South Asian 14 / 91,088 0.015% 0
      Admixed American 4 / 60,018 0.0067% 0
      European (non-Finnish) 41 / 1,180,012 0.0035% 0
      European (Finnish) 0 / 64,038
      Amish 0 / 912
      East Asian 0 / 44,876
      Middle Eastern 0 / 6,062
      Ashkenazi Jewish 0 / 29,602
      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.
      Overall AF
      26 / 282,686
      0.0092%
      Highest · African/African American
      0.06%
      Homozygotes
      0
      grpmax FAF
      0.033%
      Allele frequency by ancestry — gnomAD v2.1
      observed in 5 of 8 groups
      AncestryAllele countFrequencyHomozygotes
      African/African American 15 / 24,974 0.06% 0
      South Asian 7 / 30,616 0.023% 0
      Remaining individuals 1 / 7,218 0.014% 0
      Admixed American 1 / 35,436 0.0028% 0
      European (non-Finnish) 2 / 129,028 0.0016% 0
      Ashkenazi Jewish 0 / 10,360
      East Asian 0 / 19,930
      European (Finnish) 0 / 25,124
      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.
      This variant is absent from gnomAD-Canada.
      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.
      Literature · 23 PMIDs triaged · 8 high-priority
      23papers 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.
      23532176 ↗ functional
      The ATM signaling network in development and disease.
      The DNA damage response (DDR) rapidly recognizes DNA lesions and initiates the appropriate cellular programs to maintain genome integrity. This includes the coordination of cell cycle checkpoints, transcription, translation, DNA repair, metabolism, and cell fate decisions, such as apoptosis or senescence (Jackson and Bartek, 2009). DNA double-strand breaks (DSBs) represent one of the most cytotoxi
      BS3PP5PS3PS4
      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
      BS3PS3PS4
      26010451 ↗ functional
      Amplicon sequencing of colorectal cancer: variant calling in frozen and formalin-fixed samples.
      Next generation sequencing (NGS) is an emerging technology becoming relevant for genotyping of clinical samples. Here, we assessed the stability of amplicon sequencing from formalin-fixed paraffin-embedded (FFPE) and paired frozen samples from colorectal cancer metastases with different analysis pipelines. 212 amplicon regions in 48 cancer related genes were sequenced with Illumina MiSeq using DNA
      BS3PP5PS3PS4
      26467025 ↗ functional
      A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.
      We developed a rules-based scoring system to classify DNA variants into five categories including pathogenic, likely pathogenic, variant of uncertain significance (VUS), likely benign, and benign. Over 16,500 pathogenicity assessments on 11,894 variants from 338 genes were analyzed for pathogenicity based on prediction tools, population frequency, co-occurrence, segregation, and functional studies
      BS3PS3PS4
      27498913 ↗ splicing rna
      Monogenic and polygenic determinants of sarcoma risk: an international genetic study.
      Sarcomas are rare, phenotypically heterogeneous cancers that disproportionately affect the young. Outside rare syndromes, the nature, extent, and clinical significance of their genetic origins are not known. We aimed to investigate the genetic basis for bone and soft-tissue sarcoma seen in routine clinical practice. In this genetic study, we included 1162 patients with sarcoma from four cohorts (t
      BP7PP3PP5PS4PVS1
      27978560 ↗ functional
      Prevalence and Spectrum of Germline Cancer Susceptibility Gene Mutations Among Patients With Early-Onset Colorectal Cancer.
      Hereditary cancer syndromes infer high cancer risks and require intensive cancer surveillance, yet the prevalence and spectrum of these conditions among unselected patients with early-onset colorectal cancer (CRC) is largely undetermined. To determine the frequency and spectrum of cancer susceptibility gene mutations among patients with early-onset CRC. Overall, 450 patients diagnosed with colorec
      BS3PP5PS3PS4
      28135145 ↗ functional
      Cancer Susceptibility Gene Mutations in Individuals With Colorectal Cancer.
      Purpose Hereditary factors play an important role in colorectal cancer (CRC) risk, yet the prevalence of germline cancer susceptibility gene mutations in patients with CRC unselected for high-risk features (eg, early age at diagnosis, personal/family history of cancer or polyps, tumor microsatellite instability [MSI], mismatch repair [MMR] deficiency) is unknown. Patients and Methods We recruited
      BS3PP5PS3PS4
      29058119 ↗ functional
      Comprehensive molecular characterisation of epilepsy-associated glioneuronal tumours.
      Glioneuronal tumours are an important cause of treatment-resistant epilepsy. Subtypes of tumour are often poorly discriminated by histological features and may be difficult to diagnose due to a lack of robust diagnostic tools. This is illustrated by marked variability in the reported frequencies across different epilepsy surgical series. To address this, we used DNA methylation arrays and RNA sequ
      BS3PP5PS3PS4
      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.
      PS3PS4
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots