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ATM
Final classification
VUS
ATM c.4574T>C · p.Ile1525Thr
ATM

NM_000051.4:c.4574T>C (p.Ile1525Thr) is a rare missense variant in ATM, present at extremely low frequency in gnomAD v4.1 (10/1,614,116 alleles; grpmax FAF = 1.425×10⁻⁵).

Gene
ATM
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.4574T>C
Consequence
N/A
GRCh38
chr11:108292756 T>C
GRCh37
chr11:108163483 T>C
Basis Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework was evaluated deterministically with applied criteria: BP4 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: BP4 supporting; no rule matched the adjudicated criteria.
Classification rationale
BP4 VUS
ATM c.4574T>C

NM_000051.4:c.4574T>C (p.Ile1525Thr) is a rare missense variant in ATM, present at extremely low frequency in gnomAD v4.1 (10/1,614,116 alleles; grpmax FAF = 1.425×10⁻⁵).1 This variant has been reported in ClinVar as Uncertain Significance by 5 clinical laboratories (ClinVar ID 230535); no expert panel submission is available.2 The VCEP HBOP v1.5.0 PVS1 criterion is not applicable because this is a missense variant, not a null variant.3 Multiple lines of in silico evidence support a benign impact: REVEL score 0.116 is below the VCEP BP4 threshold (≤0.249), SpliceAI predicts no splice impact (max delta 0.06), and BayesDel score is −0.336. BP4 (supporting benign) is met.4 No variant-specific functional studies, case-control data, segregation data, or pathogenic comparator at the same residue were identified in the literature. All other applicable VCEP criteria are not met.5 Based on the VCEP HBOP v1.5.0 framework, the only criterion met is BP4_Supporting (benign). No pathogenic criteria are met. With only one supporting benign criterion and no conflicting evidence, the variant does not reach a classification threshold under the ACMG/AMP combining rules and remains a Variant of Uncertain Significance.6

BP4 VUS
3 cspec ↗pvs1_variant_assessment
4 revelspliceai ↗bayesdelcspec ↗
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
BP4 supporting Benign
The VCEP HBOP v1.5.0 BP4 rule for missense variants requires REVEL score ≤0.249. The REVEL score for c.4574T>C is 0.116, which is below the 0.249 threshold. Additionally, SpliceAI predicts no splicing impact (max delta = 0.06, ≤0.1). Multiple lines of in silico evidence suggest no damaging effect on the gene product.
REVEL = 0.116 (≤0.249 threshold met). SpliceAI max delta = 0.06 (≤0.1 threshold met). BayesDel = −0.336 (benign direction). VCEP Suppl Table S1 classifies as 'Functional'.
Assessed · not applied
Pathogenic
PS1 No known pathogenic missense variant has been established at codon 1525 of ATM.
PS3 No variant-specific experimental functional data exists for p.Ile1525Thr.
PS4 The VCEP HBOP v1.5.0 requires case-control studies demonstrating a statistically significant increase in variant prevalence in affected individuals (p≤0.05 AND OR≥2 or lower 95% CI≥1.5).
PM2 The VCEP HBOP v1.5.0 requires gnomAD v4 grpmax filtering allele frequency ≤0.001% for PM2_Supporting.
PP1 The VCEP HBOP v1.5.0 requires segregation data in affected relatives for the autosomal recessive condition (Ataxia-Telangiectasia).
PP3 The VCEP HBOP v1.5.0 requires REVEL score >0.7333 for missense variants.
Benign
BA1 The VCEP HBOP v1.5.0 requires grpmax filtering allele frequency >0.5% in gnomAD v4 for BA1 Stand-Alone.
BS1 The VCEP HBOP v1.5.0 requires grpmax filtering allele frequency >0.05% in gnomAD v4 for BS1.
BS3 The VCEP HBOP v1.5.0 requires experimental functional evidence that the variant rescues ATM-specific features (e.g.
BP2 The VCEP HBOP v1.5.0 BP2 rule requires observation of the variant in trans with a pathogenic variant in an unaffected individual ≥18 years old, or homozygous in an unaffected individual, applying the PM3/BP2 point table.
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= 6.19534e-06; MAF= 0.00062%, 10/1614116 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 4.39155e-05; MAF= 0.00439%, 4/91084 alleles, homozygotes = 0); grpmax FAF= 1.425e-05.
v2.1
This variant is present in gnomAD v2.1 (AF= 7.95646e-06; MAF= 0.00080%, 2/251368 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 6.53253e-05; MAF= 0.00653%, 2/30616 alleles, homozygotes = 0); grpmax FAF= 1.082e-05.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00062% · 10 / 1,614,116
0 hom · FAF 0.0014%
South Asian
4 / 91,084
0.0044%
European (non-Finnish)
6 / 1,179,970
0.00051%
+ 8 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.0008% · 2 / 251,368
0 hom · FAF 0.0011%
South Asian
2 / 30,616
0.0065%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals)
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 (5 clinical laboratories). (ClinVarID = 230535)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.06). REVEL score = 0.116. BayesDel score = -0.335733.
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 · 8 PMIDs not cited in assessment
16832357 ↗ ATM mutations that cause ataxia-telangiectasia are breast cancer susceptibility alleles. CLINVAR
19781682 ↗ Rare, evolutionarily unlikely missense substitutions in ATM confer increased risk of breast cancer. CLINVAR
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
24366376 ↗ Risk assessment, genetic counseling, and genetic testing for BRCA-related cancer in women: U.S. Preventive Services Task Force recommendation statement. 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
26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Versi CLINVAR
20050888 ↗ EFNS guidelines on the molecular diagnosis of ataxias and spastic paraplegias. CLINVAR