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NM_000051.4:c.4247A>G
p.Gln1416Arg · ATM
0%
complete
Final classification
VUS
PM2
ATM
c.4247A>G
p.Gln1416Arg
This variant

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%.

Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.4247A>G
GRCh38
chr11:108289612 A>G
GRCh37
chr11:108160339 A>G
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
LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
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
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
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 · 5 not met · 5 not assessed
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