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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 applied · 10 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is extremely rare in population databases. In gnomAD v4.1, the allele frequency is 8.72e-06 (0.00087%; 14/1,604,866 alleles, 0 homozygotes) with grpmax filtering AF of 6.17e-06 (0.000617%). This is well below the ATM VCEP v1.5.0 PM2_Supporting threshold of ≤0.001% in gnomAD v4. The variant is also rare in gnomAD v2.1 (AF=1.63e-05; 4/245,772 alleles).
gnomAD v4.1 AF=0.00087% (≤0.001% VCEP threshold)grpmax FAF=0.000617%14/1
Assessed · not applied
Pathogenic
PS1 PS1 requires a known (likely) pathogenic missense variant at the same nucleotide position with the same predicted amino acid change and splicing ruled out for both.
PS3 No variant-specific functional assay data were identified for NM_000051.4:c.4247A>G (p.Gln1416Arg).
PS4 No variant-specific case-control study with adequate statistical power was identified for NM_000051.4:c.4247A>G.
PP1 No segregation data were identified for NM_000051.4:c.4247A>G.
PP3 Under ATM VCEP v1.5.0, PP3 for missense variants requires a REVEL score >0.7333.
Benign
BA1 Under ATM VCEP v1.5.0, BA1 requires a grpmax filtering AF >0.5% in gnomAD v4.
BS1 Under ATM VCEP v1.5.0, BS1 requires a grpmax filtering AF >0.05% in gnomAD v4.
BS3 No variant-specific functional rescue data were identified for NM_000051.4:c.4247A>G (p.Gln1416Arg).
BP2 No co-occurrence (in trans with a pathogenic ATM variant) data were identified for NM_000051.4:c.4247A>G.
BP4 Under ATM VCEP v1.5.0, BP4 for missense variants requires a REVEL score ≤0.249.
N/A · 14 PVS1 · PS2 · PM1 · PM5 · PM6 · PP2 · PP4 · PP5 · BS2 · BS4 · BP1 · BP5 · BP6 · BP7
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