0%
complete
Final classification
VUS
PM2BP4
ATM
c.2638+11A>G
p.?
unknown · exon 17i

ATM encodes a kinase that acts as a master controller of the cellular DNA damage response: it detects double-strand breaks and coordinates DNA repair, cell cycle arrest, or apoptosis through downstream targets including p53, BRCA1, and CHK2. Loss-of-function mutations in both copies of ATM cause ataxia telangiectasia, an autosomal recessive disorder characterized by neurological problems, immune deficiency, and cancer predisposition. ATM functions as a tumor suppressor: individuals with ataxia telangiectasia are prone to childhood lymphomas, leukemias, and breast cancer, while carriers of a single altered copy have increased risk of breast, pancreatic, prostate, and other cancers. Somatic ATM mutations also occur in lymphoid malignancies and solid tumors, and ATM-deficient cancers are often especially sensitive to DNA-damaging treatments.

This variant

This ATM variant is assessed in the context of ATM's role as a tumor suppressor and master regulator of DNA-damage repair, with biallelic loss of function causing ataxia-telangiectasia and heterozygous alterations contributing to cancer predisposition.

Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.2638+11A>G
GRCh38
chr11:108267353 A>G
GRCh37
chr11:108138080 A>G
VUS: ATM VCEP Rule31 is satisfied by PM2 (supporting) and BP4 (supporting), producing Uncertain Significance - Conflicting Evidence.
Classification rationale
PM2 BP4 VUS
ATM c.2638+11A>G unknown · exon 17i

PM2 supporting: the gnomAD v4.1 grpmax FAF is 0.000739%, below the ATM VCEP 0.001% threshold. BP4 supporting: SpliceAI maximum delta score is 0.00, meeting the ATM VCEP no-splice-impact threshold.

PM2 + BP4 VUS
Gene diagram · NM_000051.4 · variants mapped to exon structure
ATM NM_000051.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 12 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 · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
Met at Supporting: gnomAD v4.1 grpmax FAF is 7.39e-06 (0.000739%), below the ≤0.001% PM2 threshold.
ClinGen HBOP ATM VCEP v1.5 specifies PM2 Supporting for frequency ≤0.001% in gnomAD v4 and states that one allele in a single subpopulation is sufficient.gnomAD v4.1 reports total AF 4.34024e-06 (0.000434%), grpmax FAF 7.39e-06 (0.000739%), 7/1,612,814 alleles, and homozygote count 0.The governing ATM specification does not require a non-cancer or exome-only subset for PM2, so the default all-comers gnomAD v4 result is used.
BP4 supporting Benign
Met, Supporting: SpliceAI maximum delta score is 0.00, meeting the ATM VCEP BP4 no-splice-impact threshold of ≤0.1.
ClinGen HBOP ATM VCEP v1.5 specifies BP4 Supporting for splicing when SpliceAI delta score is ≤0.1.SpliceAI reports maximum delta score 0.00 for NM_000051.4:c.2638+11A>G.
Assessed · not applied · 4 not met · 8 not assessed
Pathogenic
PVS1 Not met: the intronic +11 variant has a SpliceAI maximum delta score of 0.00, with no predicted splice defect or demonstrated loss-of-function consequence.
PS1 Not assessed: c.2638+11A>G has protein consequence p.? and SpliceAI max delta 0.00, without an established pathogenic splice comparator showing the same event.
PS3 Not assessed: no variant-specific ATM functional assay result is documented for NM_000051.4:c.2638+11A>G.
PS4 Not assessed: no exact-variant case-control p-value, effect estimate, or confidence interval is available to test the ATM PS4 thresholds.
PM3 Not assessed: no affected-proband, phase, or trans/cis observations are available to assign ATM VCEP PM3 points.
PM5 Not assessed: the ATM splice-specific PM5 route requires observed PVS1_VS(RNA) impact, but only SpliceAI max delta 0.00 is available.
PP1 Not assessed: no affected-relative segregation count or genotype-linked meioses are documented for this variant.
PP3 Not met: SpliceAI maximum delta score is 0.00, below the ATM VCEP PP3 splice-impact threshold of ≥0.2.
Benign
BA1 Not met: gnomAD v4.1 grpmax FAF is 7.39e-06 (0.000739%), below the >0.5% BA1 threshold.
BS1 Not met: gnomAD v4.1 grpmax FAF is 7.39e-06 (0.000739%), below the >0.05% BS1 threshold.
BS3 Not assessed: no variant-specific ATM rescue result is documented for NM_000051.4:c.2638+11A>G.
BP2 Not assessed: no unaffected adult, paired pathogenic ATM variant, or confirmed cis/trans or homozygous observation is available to assign BP2 points.
N/A · 14 PS2 · PM1 · PM4 · 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= 4.34024e-06; MAF= 0.00043%, 7/1612814 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 4.45971e-05; MAF= 0.00446%, 2/44846 alleles, homozygotes = 0); grpmax FAF= 7.39e-06.
v2.1
This variant is present in gnomAD v2.1 (AF= 3.97997e-06; MAF= 0.00040%, 1/251258 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 5.4401e-05; MAF= 0.00544%, 1/18382 alleles, homozygotes = 0).
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00043% · 7 / 1,612,814
0 hom · FAF 0.00074%
East Asian
2 / 44,846
0.0045%
Remaining individuals
1 / 62,466
0.0016%
European (non-Finnish)
4 / 1,178,994
0.00034%
+ 7 not observed (Admixed American, European (Finnish), Amish, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.0004% · 1 / 251,258
0 hom
East Asian
1 / 18,382
0.0054%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, European (Finnish), European (non-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 Likely benign (3 clinical laboratories). (ClinVarID = 384288)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
Functional No data
No calibrated functional assay or RNA evidence was identified for this variant.
OncoKB ↗
COSMIC screenshot
COSMIC
Somatic evidence
COSMIC
This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant cancer hotspot.
COSMIC ↗
Sources & reference links
8Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Triaged references · 7 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
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