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ATM
Final classification
Uncertain Significance - Conflicting Evidence
ATM c.5600A>G · p.Gln1867Arg
ATM

NM_000051.4:c.5600A>G (p.Gln1867Arg) is a missense variant in exon 37 of ATM. It has been reported in ClinVar as a variant of uncertain significance (ClinVar ID 453589, 4 clinical laboratories).

Gene
ATM
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.5600A>G
Consequence
N/A
GRCh38
chr11:108304778 A>G
GRCh37
chr11:108175505 A>G
Basis Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework: matched Rule31 (Benign.Supporting >=1 + Pathogenic.Supporting >=1) with applied criteria: PS3 supporting, PM2 supporting, BP4 supporting; maps to Uncertain Significance - Conflicting Evidence.
Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework: matched Rule31 (Benign.Supporting >=1 + Pathogenic.Supporting >=1) with applied criteria: PS3 supporting, PM2 supporting, BP4 supporting; maps to Uncertain Significance - Conflicting Evidence.
Classification rationale
PS3PM2 BP4 Uncertain Significance - Conflicting Evidence
ATM c.5600A>G

NM_000051.4:c.5600A>G (p.Gln1867Arg) is a missense variant in exon 37 of ATM. It has been reported in ClinVar as a variant of uncertain significance (ClinVar ID 453589, 4 clinical laboratories).1 This variant is present in gnomAD v4.1 at an extremely low allele frequency (AF = 1.86e-6, 3/1,613,944 alleles, 0 homozygotes) and is absent from gnomAD v2.1 and gnomAD-Canada, meeting the ATM VCEP PM2_Supporting threshold (≤0.001%).2 The ATM VCEP supplementary functional data (Suppl_TableS1, PMID 40580951) classifies this variant as 'Non-functional' (combined score -2.05, Medium-high confidence), meeting PS3_Supporting per the VCEP framework for variants that fail to rescue ATM-specific functional features.3 Multiple computational predictors suggest a benign effect: REVEL score 0.088 (meeting BP4_Supporting threshold ≤0.249), BayesDel -0.34033, AlphaMissense 0.0758. SpliceAI predicts no splicing impact (max delta 0.10, meeting BP4 splicing threshold ≤0.1).4 No case-control studies, co-segregation data, or confirmed de novo observations have been identified for this variant. A ClinVar submission noting observation in trans with a pathogenic ATM variant in an A-T patient was not accompanied by peer-reviewed publication, precluding application of PM3.5 The variant has not been reported in COSMIC and is not located in a statistically significant cancer hotspot residue.

PS3 + PM2 + BP4 Uncertain Significance - Conflicting Evidence
3 vcep_suppl_tables1_pmid_40580951
4 revelbayesdelspliceai ↗
Gene diagram · NM_000051.4 · variants mapped to exon structure
ATM NM_000051.4
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 8 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PS3 supporting Pathogenic
The ATM VCEP supplementary functional data (Suppl_TableS1, PMID 40580951) classifies NM_000051.4:c.5600A>G (p.Q1867R) as 'Non-functional' with Medium-high confidence based on a combined function score of -2.05 integrating multiple functional predictors. This meets the VCEP PS3_Supporting threshold for a variant that fails to rescue an ATM-specific functional feature. No direct experimental rescue assay data (kinase activity or radiosensitivity) from the VCEP-approved functional studies (Mitui 2009, Barone 2009, Scott 2002) was identified for this exact variant.
Suppl_TableS1 (PMID 40580951): Combined_score -2.05Classification 'Non-functional'Confidence 'Medium-high'
PM2 supporting Pathogenic
NM_000051.4:c.5600A>G is present at an extremely low frequency in gnomAD v4.1 (AF = 1.8588e-06, 0.000186%, 3/1,613,944 alleles, 0 homozygotes). This is below the VCEP PM2_Supporting threshold of ≤0.001% (≤1e-5). The variant is absent from gnomAD v2.1 and gnomAD-Canada.
gnomAD v4.1: 3/1613944 alleles (AF 1.8588e-06)
BP4 supporting Benign
The ATM VCEP BP4 threshold for missense variants is REVEL ≤ 0.249. NM_000051.4:c.5600A>G (p.Q1867R) has a REVEL score of 0.088, meeting the BP4_Supporting threshold. Additionally, the SpliceAI max delta score is 0.10, which is ≤0.1, meeting the VCEP BP4 splicing threshold (no predicted splicing impact). BayesDel score of -0.34033 also supports a benign computational prediction.
REVEL 0.088 ≤ 0.249 (BP4 threshold for missense)SpliceAI max delta 0.10 ≤ 0.1 (no predicted splicing impact)BayesDel -0.34033.
Assessed · not applied
Pathogenic
PS1 PS1 requires the same amino acid change (p.Gln1867Arg) to be produced by a different nucleotide change already classified as pathogenic or likely pathogenic.
PS4 The ATM VCEP requires case-control studies demonstrating a statistically significant enrichment (p ≤ 0.05 AND OR ≥ 2 or lower 95% CI ≥ 1.5).
PP1 The ATM VCEP applies PP1 only for autosomal recessive conditions (Ataxia-Telangiectasia) and requires segregation of both variants in affected relatives.
PP3 The ATM VCEP PP3 threshold for missense variants is REVEL > 0.7333.
Benign
BA1 The ATM VCEP BA1 threshold requires a Grpmax Filtering AF > 0.5% in the gnomAD v4 dataset.
BS1 The ATM VCEP BS1 threshold requires a Grpmax Filtering AF > 0.05% in gnomAD v4.
BS3 The ATM VCEP BS3 requires a well-established functional assay demonstrating no damaging effect (variant rescues ATM function).
BP2 The ATM VCEP BP2 requires observation of the variant in cis with a pathogenic/likely pathogenic variant in an unaffected individual aged ≥18 years with no evidence of A-T, scored via the PM3/BP2 points table.
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= 1.8588e-06; MAF= 0.00019%, 3/1613944 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 1.60051e-05; MAF= 0.00160%, 1/62480 alleles, homozygotes = 0).
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
This variant is absent from gnomAD-Canada.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00019% · 3 / 1,613,944
0 hom
Remaining individuals
1 / 62,480
0.0016%
South Asian
1 / 91,090
0.0011%
European (non-Finnish)
1 / 1,180,002
8.5e-05%
+ 7 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, African/African American)
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
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 (4 clinical laboratories). (ClinVarID = 453589)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.10). REVEL score = 0.088. BayesDel score = -0.34033.
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 · 10 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
20301317 ↗ Hereditary Ataxia Overview. CLINVAR
20301790 ↗ Ataxia-Telangiectasia. CLINVAR
24418350 ↗ EFNS/ENS Consensus on the diagnosis and management of chronic ataxias in adulthood. CLINVAR
25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
26389210 ↗ Genetics of Breast and Gynecologic Cancers (PDQ®): Health Professional Version. CLINVAR
26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version. CLINVAR
29939840 ↗ Recommendations on Disease Management for Patients With Advanced Human Epidermal Growth Factor Receptor 2-Positive Breast Cancer and Brain Metastases: ASCO Clinical Practice Guideline Update. CLINVAR
20050888 ↗ EFNS guidelines on the molecular diagnosis of ataxias and spastic paraplegias. CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR