Starting
Initialising…
0%
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 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      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