Starting
Initialising…
0%
ATM
Final classification
VUS
ATM c.1009C>T · p.Arg337Cys
ATM

NM_000051.4:c.1009C>T (p.Arg337Cys) is a missense variant in ATM exon 8.

Gene
ATM
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.1009C>T
Consequence
N/A
GRCh38
chr11:108247071 C>T
GRCh37
chr11:108117798 C>T
Basis Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework was evaluated deterministically with applied criteria: BS3 supporting benign; no rule matched the adjudicated criteria.
Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework was evaluated deterministically with applied criteria: BS3 supporting benign; no rule matched the adjudicated criteria.
Classification rationale
BS3 VUS
ATM c.1009C>T

NM_000051.4:c.1009C>T (p.Arg337Cys) is a missense variant in ATM exon 8. This variant is present in gnomAD v4.1 at an overall allele frequency of 0.00892% (144/1,613,688 alleles, 0 homozygotes) with a grpmax filtering allele frequency of 0.021% in the Admixed American population.1 This variant does not meet PM2_Supporting (frequency ≤0.001% required), BS1 (>0.05% required), or BA1 (>0.5% required) under ATM VCEP population thresholds.2 This variant has been reported in ClinVar (Variation ID 127327) as Uncertain Significance by 18 clinical laboratories and as Likely Benign by 3 clinical laboratories; no submitter classifies it as pathogenic.3 The variant has been reported 80 times in somatic cancers (COSMIC COSV53723836) and OncoKB classifies it as Likely Oncogenic with a loss-of-function effect in the somatic context.4 Computational predictors do not support a deleterious effect: REVEL score is 0.36 (VCEP PP3 threshold >0.7333, BP4 threshold ≤0.249), SpliceAI max delta is 0.10, and BayesDel is 0.067.5 The ATM VCEP functional dataset (Suppl_TableS1, PMID 40580951) classifies this variant as 'Functional' (combined score -0.65, high confidence) based on integrated functional and evolutionary scores, meeting BS3_Supporting under VCEP rules.6 PVS1, PS1, PS2, PM1, PM5, PM6, PP2, PP4, PP5, BS2, BS4, BP1, BP5, BP6, and BP7 are not applicable under ATM VCEP v1.5.0 for this variant type.7 No case-control study demonstrates enrichment of this variant in affected individuals (PS4 not met), and no segregation data are available (PP1 not assessed).8 With only BS3_Supporting met and no pathogenic criteria fulfilled, the evidence is insufficient to classify this variant as either likely benign or likely pathogenic; the variant remains a Variant of Uncertain Significance under the ATM VCEP framework.9

BS3 VUS
5 revelspliceai ↗bayesdel
6 vcep_suppl_tables1_pmid_40580951vcep_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
      144 / 1,613,688
      0.0089%
      Highest · Admixed American
      0.032%
      Homozygotes
      0
      grpmax FAF
      0.021%
      Allele frequency by ancestry — gnomAD v4.1
      observed in 6 of 9 groups
      AncestryAllele countFrequencyHomozygotes
      Admixed American 19 / 59,982 0.032% 0
      Middle Eastern 1 / 6,080 0.016% 0
      European (non-Finnish) 108 / 1,179,910 0.0092% 0
      South Asian 7 / 91,048 0.0077% 0
      African/African American 3 / 74,886 0.004% 0
      East Asian 1 / 44,822 0.0022% 0
      European (Finnish) 0 / 63,990
      Amish 0 / 912
      Ashkenazi Jewish 0 / 29,594
      This variant is present in gnomAD v4.1 (AF= 8.92366e-05; MAF= 0.00892%, 144/1613688 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 0.000316762; MAF= 0.03168%, 19/59982 alleles, homozygotes = 0); grpmax FAF= 0.00020684.
      Overall AF
      26 / 282,550
      0.0092%
      Highest · Admixed American
      0.02%
      Homozygotes
      0
      grpmax FAF
      0.0095%
      Allele frequency by ancestry — gnomAD v2.1
      observed in 6 of 8 groups
      AncestryAllele countFrequencyHomozygotes
      Admixed American 7 / 35,394 0.02% 0
      Remaining individuals 1 / 7,214 0.014% 0
      European (non-Finnish) 14 / 128,966 0.011% 0
      South Asian 2 / 30,612 0.0065% 0
      East Asian 1 / 19,944 0.005% 0
      African/African American 1 / 24,942 0.004% 0
      Ashkenazi Jewish 0 / 10,366
      European (Finnish) 0 / 25,112
      This variant is present in gnomAD v2.1 (AF= 9.20191e-05; MAF= 0.00920%, 26/282550 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 0.000197774; MAF= 0.01978%, 7/35394 alleles, homozygotes = 0); grpmax FAF= 9.483e-05.
      This variant is absent from gnomAD-Canada.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (18 clinical laboratories) and as Likely benign (3 clinical laboratories). (ClinVarID = 127327)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.10). REVEL score = 0.36. BayesDel score = 0.0673325.
      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 Hotspot
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV53723836, n = 80 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Literature · 34 PMIDs triaged · 8 high-priority
      34papers 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.
      16014569 ↗ functional
      Mutations in the ATM gene lead to impaired overall and treatment-free survival that is independent of IGVH mutation status in patients with B-CLL.
      The ataxia telangiectasia mutated (ATM) protein is the principal activator of the p53 protein in the response to DNA double-strand breaks. Mutations in the ATM gene have been previously found in B-cell chronic lymphocytic leukemias (B-CLLs) but their clinical significance is unknown. We analyzed 155 CLL tumors and found 12% with ATM mutations and 4% with TP53 mutations; 2 tumors contained mutation
      BS3PM1PS3
      19781682 ↗ splicing rna
      Rare, evolutionarily unlikely missense substitutions in ATM confer increased risk of breast cancer.
      The susceptibility gene for ataxia telangiectasia, ATM, is also an intermediate-risk breast-cancer-susceptibility gene. However, the spectrum and frequency distribution of ATM mutations that confer increased risk of breast cancer have been controversial. To assess the contribution of rare variants in this gene to risk of breast cancer, we pooled data from seven published ATM case-control mutation-
      BP7PP3PP5PS4PVS1
      20305132 ↗ splicing rna
      Radiation exposure, the ATM Gene, and contralateral breast cancer in the women's environmental cancer and radiation epidemiology study.
      Ionizing radiation is a known mutagen and an established breast carcinogen. The ATM gene is a key regulator of cellular responses to the DNA damage induced by ionizing radiation. We investigated whether genetic variants in ATM play a clinically significant role in radiation-induced contralateral breast cancer in women. The Women's Environmental, Cancer, and Radiation Epidemiology Study is an inter
      BP7PP3PP5PS4PVS1
      22529920 ↗ functional
      Computational refinement of functional single nucleotide polymorphisms associated with ATM gene.
      Understanding and predicting molecular basis of disease is one of the major challenges in modern biology and medicine. SNPs associated with complex disorders can create, destroy, or modify protein coding sites. Single amino acid substitutions in the ATM gene are the most common forms of genetic variations that account for various forms of cancer. However, the extent to which SNPs interferes with t
      BS3PP5PS3PS4
      23555315 ↗ functional
      Genome-wide testing of putative functional exonic variants in relationship with breast and prostate cancer risk in a multiethnic population.
      Rare variation in protein coding sequence is poorly captured by GWAS arrays and has been hypothesized to contribute to disease heritability. Using the Illumina HumanExome SNP array, we successfully genotyped 191,032 common and rare non-synonymous, splice site, or nonsense variants in a multiethnic sample of 2,984 breast cancer cases, 4,376 prostate cancer cases, and 7,545 controls. In breast cance
      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
      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
      27844328 ↗ splicing rna
      Molecular Profiling of Thymoma and Thymic Carcinoma: Genetic Differences and Potential Novel Therapeutic Targets.
      Thymoma and thymic carcinoma are thymic epithelial tumors (TETs). We performed a molecular profiling to investigate the pathogenesis of TETs and identify novel targets for therapy. We analyzed 37 thymomas (18 type A, 19 type B3) and 35 thymic carcinomas. The sequencing of 50 genes detected nonsynonymous mutations in 16 carcinomas affecting ALK, ATM, CDKN2A, ERBB4, FGFR3, KIT, NRAS and TP53. Only t
      BP7PP3PP5PS4PVS1
      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