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NM_000051.4:c.2377-18T>C
p.? · ATM
0%
complete
Final classification
VUS
BP4
ATM
c.2377-18T>C
p.?
unknown · exon 15i

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

ATM encodes a DNA-damage-response kinase and tumor suppressor, and loss of ATM function underlies ataxia-telangiectasia and contributes to inherited cancer susceptibility.

Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.2377-18T>C
GRCh38
chr11:108258968 T>C
GRCh37
chr11:108129695 T>C
VUS: BP4 (supporting) indicates no predicted splice impact, but no pathogenic or benign combination rule is satisfied under the ATM VCEP framework.
Classification rationale
BP4 VUS
ATM c.2377-18T>C unknown · exon 15i

BP4 supporting: SpliceAI maximum delta 0.059 is below the ATM VCEP threshold of 0.1 for no predicted splice impact.

BP4 → 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 · 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 · 1
Strength Supporting Moderate Strong Very strong
BP4 supporting Benign
Met at supporting: SpliceAI maximum delta 0.059 meets the ATM VCEP BP4 splicing threshold of <=0.1.
ClinGen HBOP ATM VCEP Version 1.6 assigns BP4 Supporting for splicing when SpliceAI is <=0.1; the variant is intronic and therefore uses the SpliceAI path.The case SpliceAI result reports DS_AG 0.007, DS_AL 0.059, DS_DG 0.000, and DS_DL 0.055, with maximum delta 0.059.The governing Suppl_TableS1_PMID 40580951 full-text conversion was searched for c.2377-18T>C, c.2377-18, 2377-18, and p.?; no exact entry was found, so no pre-assigned BP4 code was available from that file.
Assessed · not applied · 5 not met · 7 not assessed
Pathogenic
PVS1 Not met: the intronic -18 variant is outside canonical splice positions, lacks RNA evidence, and has SpliceAI maximum delta 0.059.
PS1 Not assessed: SpliceAI max delta is 0.059, but no qualifying same-event P/LP reference entry was found for PS1 comparison.
PS3 Not assessed: no variant-specific ATM kinase or radiosensitivity result was found in the governing approved-assay sources for c.2377-18T>C.
PS4 Not assessed: no variant-specific case-control p-value, effect estimate, or confidence interval is available to evaluate the ATM PS4 thresholds.
PM2 Not met: gnomAD v4.1 East Asian AF is 2.2346e-05 (0.00223%), above the ATM VCEP PM2 threshold of <=0.001%.
PM3 Not assessed: no affected-proband, homozygous, second-allele, or phase evidence is available to assign the ATM VCEP's PM3 points.
PP1 Not assessed: no affected-relative segregation, parental testing, phase, or meiosis data are documented to meet the ATM PP1 thresholds.
PP3 Not met: SpliceAI maximum delta 0.059 is below the ATM VCEP PP3 splicing threshold of >=0.2.
Benign
BA1 Not met: gnomAD v4.1 grpmax filtering AF is 5.49e-06, below the ATM VCEP BA1 threshold of >0.005.
BS1 Not met: gnomAD v4.1 grpmax filtering AF is 5.49e-06, below the ATM VCEP BS1 threshold of >0.0005.
BS3 Not assessed: no variant-specific ATM rescue or normal-function result was found in the governing approved-assay sources for c.2377-18T>C.
BP2 Not assessed: no unaffected adult carrying this variant with a pathogenic ATM allele in trans or qualifying homozygous observation is documented.
N/A · 15 PS2 · PM1 · 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= 9.38964e-06; MAF= 0.00094%, 15/1597506 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 2.23464e-05; MAF= 0.00223%, 1/44750 alleles, homozygotes = 0); grpmax FAF= 5.49e-06.
v2.1
This variant is present in gnomAD v2.1 (AF= 1.9931e-05; MAF= 0.00199%, 5/250866 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.52454e-05; MAF= 0.00352%, 4/113490 alleles, homozygotes = 0); grpmax FAF= 1.123e-05.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00094% · 15 / 1,597,506
0 hom · FAF 0.00055%
East Asian
1 / 44,750
0.0022%
Remaining individuals
1 / 61,932
0.0016%
South Asian
1 / 90,724
0.0011%
European (non-Finnish)
12 / 1,165,318
0.001%
+ 6 not observed (Admixed American, European (Finnish), Amish, Middle Eastern, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.002% · 5 / 250,866
0 hom · FAF 0.0011%
European (non-Finnish)
4 / 113,490
0.0035%
South Asian
1 / 30,554
0.0033%
+ 6 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (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 Likely benign (5 clinical laboratories). (ClinVarID = 381894)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.06).
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
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
18163131 ↗ The emerging landscape of breast cancer susceptibility. CLINVAR
20301425 ↗ BRCA1- and BRCA2-Associated Hereditary Breast and Ovarian Cancer. CLINVAR
34012068 ↗ ACMG SF v3.0 list for reporting of secondary findings in clinical exome and genome sequencing: a policy statement of the American College of Medical Genetics and Genomics (ACMG). CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR