Starting
Initialising…
0%
ATM
Final classification
VUS
ATM c.4247A>G · p.Gln1416Arg
ATM

NM_000051.4:c.4247A>G (p.Gln1416Arg) is a rare missense variant in ATM with an allele frequency of 0.00087% in gnomAD v4.1 (14/1,604,866 alleles, 0 homozygotes), meeting PM2_Supporting under the ClinGen HBOP VCEP v1.5.0 threshold of ≤0.001%.

Gene
ATM
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.4247A>G
Consequence
N/A
GRCh38
chr11:108289612 A>G
GRCh37
chr11:108160339 A>G
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.4247A>G

NM_000051.4:c.4247A>G (p.Gln1416Arg) is a rare missense variant in ATM with an allele frequency of 0.00087% in gnomAD v4.1 (14/1,604,866 alleles, 0 homozygotes), meeting PM2_Supporting under the ClinGen HBOP VCEP v1.5.0 threshold of ≤0.001%.1 Computational predictors are inconclusive: REVEL score of 0.45 falls between the VCEP thresholds for PP3 (>0.7333) and BP4 (≤0.249), and BayesDel score of -0.0913068 is weakly benign. SpliceAI predicts no splicing impact (max delta=0.04). Neither PP3 nor BP4 is met.2 This variant has been reported in ClinVar as Uncertain Significance by 6 clinical laboratories (ClinVar Variation ID: 230064, review status: criteria provided, single submitter). No expert panel classification has been recorded.3 No variant-specific functional data (PS3/BS3), case-control studies (PS4), segregation data (PP1), or co-occurrence data (BP2) were identified for this variant. OncoKB reports Unknown Oncogenic Effect. The variant has not been reported in COSMIC.4 With only PM2_Supporting met and no pathogenic moderate/strong/very strong criteria fulfilled, this variant is classified as a Variant of Uncertain Significance (VUS) under the ACMG/AMP framework as specified by the ClinGen HBOP VCEP for ATM v1.5.0.5

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= 8.72347e-06; MAF= 0.00087%, 14/1604866 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 1.6129e-05; MAF= 0.00161%, 1/62000 alleles, homozygotes = 0); grpmax FAF= 6.17e-06.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 1.62752e-05; MAF= 0.00163%, 4/245772 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.57961e-05; MAF= 0.00358%, 4/111744 alleles, homozygotes = 0); grpmax FAF= 1.136e-05.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00087% · 14 / 1,604,866
      0 hom · FAF 0.00062%
      Remaining individuals
      1 / 62,000
      0.0016%
      European (non-Finnish)
      13 / 1,175,936
      0.0011%
      + 8 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0016% · 4 / 245,772
      0 hom · FAF 0.0011%
      European (non-Finnish)
      4 / 111,744
      0.0036%
      + 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 = 230064)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04). REVEL score = 0.45. BayesDel score = -0.0913068.
      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
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 9 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
      28779002 ↗ Rare, protein-truncating variants in ATM, CHEK2 and PALB2, but not XRCC2, are associated with increased breast cancer risks. 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
      20301425 ↗ BRCA1- and BRCA2-Associated Hereditary Breast and Ovarian Cancer. CLINVAR
      20301790 ↗ PMID:20301790 CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR