Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
ATM
Final classification
Likely Benign
ATM c.6572+11C>T · p.?
ATM

NM_000051.4:c.6572+11C>T is an intronic variant located at position +11 in intron 45 of ATM, outside the canonical splice donor site. SpliceAI predicts no splicing impact (max delta score = 0.00), satisfying BP4 (supporting). The variant position at +11 is further than +7 from the donor site, meeting the ATM VCEP definition of a deep intronic variant for BP7 (supporting).

Gene
ATM
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.6572+11C>T
Consequence
N/A
GRCh38
chr11:108321431 C>T
GRCh37
chr11:108192158 C>T
Basis Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework: matched Rule19 (Benign.Supporting >=2) with applied criteria: BP4 supporting, BP7 supporting; maps to Likely Benign.
Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework: matched Rule19 (Benign.Supporting >=2) with applied criteria: BP4 supporting, BP7 supporting; maps to Likely Benign.
Classification rationale
BP4BP7 Likely Benign
ATM c.6572+11C>T

NM_000051.4:c.6572+11C>T is an intronic variant located at position +11 in intron 45 of ATM, outside the canonical splice donor site. SpliceAI predicts no splicing impact (max delta score = 0.00), satisfying BP4 (supporting). The variant position at +11 is further than +7 from the donor site, meeting the ATM VCEP definition of a deep intronic variant for BP7 (supporting).1 This variant is present in gnomAD v4.1 at an allele frequency of 0.00818% (132/1,613,760 alleles; grpmax FAF = 0.0102%) and in gnomAD v2.1 at 0.00495% (14/282,814 alleles). The frequency exceeds the VCEP PM2_Supporting threshold of ≤0.001% but does not reach BS1 (>0.05%) or BA1 (>0.5%) thresholds.2 This variant has been reported in ClinVar as Likely benign by four clinical laboratories and as Benign by one clinical laboratory (ClinVar Variation ID: 490663). While ClinVar consensus favors a benign interpretation, the ATM VCEP does not permit use of BP6, and this evidence is noted for context only.3 No functional studies, case-control data, segregation data, or de novo observations were identified for this variant. PVS1 is not applicable as the variant lies outside the canonical ±1,2 splice sites. PS1 cannot be applied without a PP3 baseline (SpliceAI <0.2).4 Applying the ATM VCEP v1.5.0 ACMG/AMP combination rules: BP4_Supporting and BP7_Supporting are both met (2 benign supporting criteria). Rule 19 (≥2 Benign Supporting) yields a classification of Likely Benign.5

BP4 + BP7 Likely Benign
Gene diagram · NM_000051.4 · variants mapped to exon structure
ATM NM_000051.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 11 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
BP4 supporting Benign
SpliceAI predicts no splicing impact for this intronic variant (max delta = 0.00). This meets the ATM VCEP BP4_Supporting threshold for splicing (SpliceAI ≤0.1).
SpliceAI max delta = 0.00no predicted splicing impact
BP7 supporting Benign
NM_000051.4:c.6572+11C>T is an intronic variant at position +11, which is further than +7 from the donor site. The ATM VCEP BP7 rule applies to deep intronic variants defined as further than (but not including) +7 at donor sites. SpliceAI predicts no splicing impact (max delta = 0.00), consistent with a lack of aberrant splicing.
Intronic variant at +11further than +7 from donor siteSpliceAI max delta = 0.00
Assessed · not applied
Pathogenic
PVS1 NM_000051.4:c.6572+11C>T is an intronic variant at position +11, outside the canonical ±1,2 splice donor/acceptor dinucleotides.
PS1 The ATM PS1 splicing table requires a PP3 baseline (SpliceAI ≥0.2) for variants located outside donor/acceptor ±1,2 positions.
PS3 No functional studies evaluating ATM kinase activity or radiosensitivity rescue for NM_000051.4:c.6572+11C>T were identified.
PS4 No case-control studies with adequate statistical power were identified for NM_000051.4:c.6572+11C>T.
PM2 The ATM VCEP PM2_Supporting threshold is ≤0.001% (≤0.00001) in gnomAD v4.
PP1 No segregation data in affected relatives was identified for NM_000051.4:c.6572+11C>T.
PP3 The ATM VCEP PP3 threshold for splicing prediction is SpliceAI ≥0.2 for intronic variants outside donor/acceptor ±1,2 sites.
Benign
BA1 The ATM VCEP BA1 (Stand Alone) threshold is grpmax filtering AF >0.5% in gnomAD v4.
BS1 The ATM VCEP BS1 (Benign Strong) threshold is grpmax filtering AF >0.05% in gnomAD v4.
BS3 No functional studies demonstrating rescue of ATM-specific features and/or radiosensitivity were identified for NM_000051.4:c.6572+11C>T.
BP2 No proband data for unaffected individuals (≥18 years, no A-T) with this variant observed in trans or homozygous with a pathogenic/likely pathogenic ATM variant was identified.
N/A · 15 PS2 · PM1 · PM3 · PM4 · PM5 · PM6 · PP2 · PP4 · PP5 · BS2 · BS4 · BP1 · BP3 · BP5 · BP6
Research & evidence
Population frequency · supports benign
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= 8.17965e-05; MAF= 0.00818%, 132/1613760 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 0.000183388; MAF= 0.01834%, 11/59982 alleles, homozygotes = 0); grpmax FAF= 0.00010205.
v2.1
This variant is present in gnomAD v2.1 (AF= 4.95025e-05; MAF= 0.00495%, 14/282814 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 0.000112867; MAF= 0.01129%, 4/35440 alleles, homozygotes = 0); grpmax FAF= 3.893e-05.
🇨🇦 CA
This variant is absent from gnomAD-Canada.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.0082% · 132 / 1,613,760
0 hom · FAF 0.01%
Admixed American
11 / 59,982
0.018%
European (non-Finnish)
110 / 1,179,928
0.0093%
African/African American
4 / 74,860
0.0053%
East Asian
2 / 44,882
0.0045%
South Asian
3 / 91,070
0.0033%
Remaining individuals
1 / 62,476
0.0016%
European (Finnish)
1 / 63,968
0.0016%
+ 3 not observed (Amish, Middle Eastern, Ashkenazi Jewish)
gnomAD v2.1
0.005% · 14 / 282,814
0 hom · FAF 0.0039%
Admixed American
4 / 35,440
0.011%
European (non-Finnish)
9 / 129,148
0.007%
African/African American
1 / 24,956
0.004%
+ 5 not observed (Ashkenazi Jewish, East Asian, European (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 (4 clinical laboratories) and as Benign (1 clinical laboratory). (ClinVarID = 490663)
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
7Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
SpliceAI
OncoKB
COSMIC
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
28779002 ↗ Rare, protein-truncating variants in ATM, CHEK2 and PALB2, but not XRCC2, are associated with increased breast cancer risks. 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
17508274 ↗ Risk assessment and genetic counseling for hereditary breast and ovarian cancer: recommendations of the National Society of Genetic Counselors. CLINVAR
18163131 ↗ The emerging landscape of breast cancer susceptibility. CLINVAR
20301317 ↗ PMID:20301317 CLINVAR
20301425 ↗ BRCA1- and BRCA2-Associated Hereditary Breast and Ovarian Cancer. 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