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ATM
Final classification
Uncertain Significance - Conflicting Evidence
ATM c.7486G>C · p.Gly2496Arg
ATM

NM_000051.4:c.7486G>C (p.Gly2496Arg) is a missense variant in ATM exon 50.

Gene
ATM
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.7486G>C
Consequence
N/A
GRCh38
chr11:108330392 G>C
GRCh37
chr11:108201119 G>C
Basis Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework: matched Rule31 (Benign.Supporting >=1 + Pathogenic.Supporting >=1) with applied criteria: 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: PM2 supporting, BP4 supporting; maps to Uncertain Significance - Conflicting Evidence.
Classification rationale
PM2 BP4 Uncertain Significance - Conflicting Evidence
ATM c.7486G>C

NM_000051.4:c.7486G>C (p.Gly2496Arg) is a missense variant in ATM exon 50. This variant is extremely rare in population databases: present in gnomAD v4.1 at an allele frequency of 0.00037% (6/1,614,098 alleles, 0 homozygotes), meeting the VCEP threshold for PM2_Supporting.1 Multiple lines of computational evidence suggest a benign effect: REVEL score is 0.189 (meeting the VCEP BP4 threshold of ≤0.249), BayesDel score is negative (-0.183511), and SpliceAI predicts no splicing impact (max delta 0.04). BP4_Supporting is applied.2 The ATM VCEP supplementary in silico meta-predictor (Suppl_TableS1, PMID:40580951) classifies this variant as 'Functional' with High confidence (Combined score 0.962), consistent with the benign computational evidence.3 This variant has been reported in ClinVar as Uncertain significance by three clinical laboratories (Variation ID: 569749).4 PVS1, PS1, PM1, PM5, PM6, PS2, PP1, PP2, PP4, PP5, BS2, BS4, BP1, BP5, BP6, and BP7 are not applicable per ATM VCEP v1.5.0 specifications.5 No variant-specific experimental functional studies, case-control data, or segregation data were identified for this variant. Applying the ATM VCEP v1.5.0 classification framework: PM2_Supporting (1 pathogenic supporting point) and BP4_Supporting (1 benign supporting point). Per the generic ACMG/AMP 2015 combination rules (Rule 31), one pathogenic supporting criterion and one benign supporting criterion result in conflicting evidence, yielding an overall classification of Uncertain Significance.6

PM2 + BP4 Uncertain Significance - Conflicting Evidence
2 revelbayesdelspliceai ↗
3 vcep_suppl_tables1_pmid_40580951
Gene diagram · NM_000051.4 · variants mapped to exon structure
ATM NM_000051.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 9 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_000051.4:c.7486G>C is extremely rare in population databases. In gnomAD v4.1, the variant is present at an allele frequency of 0.00037% (6/1,614,098 alleles, 0 homozygotes), with a grpmax filtering AF of 1.83e-06. This frequency (≤0.001%) meets the ATM VCEP threshold for PM2_Supporting.
gnomAD v4.1: 6/1614098 alleles (AF=3.72e-06
BP4 supporting Benign
BP4 for missense variants under ATM VCEP requires REVEL score ≤0.249. The REVEL score for NM_000051.4:c.7486G>C is 0.189, meeting this threshold. Additionally, BayesDel score is negative (-0.183511) and SpliceAI max delta is 0.04 (≤0.1), indicating no predicted splicing impact. Multiple lines of computational evidence suggest no damaging effect on the gene product.
REVEL=0.189 (≤0.249 threshold met)BayesDel=-0.183511SpliceAI max delta=0.04 (≤0.1
Assessed · not applied
Pathogenic
PS1 PS1 requires a previously established pathogenic or likely pathogenic variant causing the same amino acid change.
PS3 No variant-specific experimental functional studies (well-established in vitro or in vivo assays) were identified for NM_000051.4:c.7486G>C.
PS4 PS4 requires case-control studies demonstrating statistically significant enrichment of the variant in affected individuals (p≤0.05, OR/HR/RR ≥2 or lower 95% CI ≥1.5).
PP1 PP1 requires co-segregation of the variant with disease in affected family members.
PP3 PP3 for missense variants under ATM VCEP requires REVEL score >0.7333.
Benign
BA1 BA1 requires grpmax filtering AF >0.5% in gnomAD v4.
BS1 BS1 requires grpmax filtering AF >0.05% in gnomAD v4.
BS3 No variant-specific experimental functional studies demonstrating no damaging effect were identified for NM_000051.4:c.7486G>C.
BP2 BP2 requires observation of the variant in trans with a pathogenic variant in an unaffected individual (≥18 years, no evidence of A-T).
N/A · 17 PVS1 · PS2 · PM1 · PM3 · PM4 · PM5 · PM6 · PP2 · PP4 · PP5 · BS2 · BS4 · BP1 · BP3 · 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= 3.71725e-06; MAF= 0.00037%, 6/1614098 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 5.08477e-06; MAF= 0.00051%, 6/1179994 alleles, homozygotes = 0); grpmax FAF= 1.83e-06.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00037% · 6 / 1,614,098
0 hom · FAF 0.00018%
European (non-Finnish)
6 / 1,179,994
0.00051%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, 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 (3 clinical laboratories). (ClinVarID = 569749)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04). REVEL score = 0.189. BayesDel score = -0.183511.
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
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 5 PMIDs not cited in assessment
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
20050888 ↗ EFNS guidelines on the molecular diagnosis of ataxias and spastic paraplegias. CLINVAR