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ATM
Final classification
VUS
ATM c.5544T>C · p.Asp1848=
ATM

NM_000051.3:c.5544T>C (NP_000042.3:p.(Asp1848=)) is a synonymous variant in ATM exon 36, assessed using the ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer (HBOP) Expert Panel specifications for ATM v1.5.0.

Gene
ATM
Transcript
NM_000051.3
HGVS · transcript:coding
NM_000051.3:c.5544T>C
Consequence
N/A
GRCh38
chr11:108304722 T>C
GRCh37
chr11:108175449 T>C
Basis Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting, BP4 supporting benign, BP6 supporting benign, BP7 supporting benign; no rule matched the adjudicated criteria.
Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting, BP4 supporting benign, BP6 supporting benign, BP7 supporting benign; no rule matched the adjudicated criteria.
Classification rationale
PM2 BP4BP6BP7 VUS
ATM c.5544T>C

NM_000051.3:c.5544T>C (NP_000042.3:p.(Asp1848=)) is a synonymous variant in ATM exon 36, assessed using the ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer (HBOP) Expert Panel specifications for ATM v1.5.0.1 The variant is absent or exceedingly rare in population databases: gnomAD v4.1 global allele frequency 6.20×10⁻⁷ (1/1,613,962 alleles, 0 homozygotes) and gnomAD v2.1 allele frequency 7.97×10⁻⁶ (2/251,006 alleles, 0 homozygotes), satisfying PM2_Supporting (≤0.001% cutoff).2 SpliceAI predicts no significant splicing impact (max delta = 0.06), satisfying BP4_Supporting (SpliceAI ≤0.1 for no predicted splicing impact) under the CSPEC HBOP splicing rule.3 BP7_Supporting is applied: the variant is a synonymous substitution located at c.5544, which lies 18 nucleotides from the donor splice site (beyond the +7 boundary) and 153 nucleotides from the acceptor splice site (beyond the -21 boundary), meeting the CSPEC definition for synonymous variants outside donor/acceptor site boundaries.4 REVEL, BayesDel, and HCI Prior scores are not available for this synonymous variant, so the missense-specific in silico rules (PP3 missense, BP4 missense) are not applicable. ClinVar classifies this variant as Likely Benign (VariationID 184944, reviewed by the ClinGen HBOP Expert Panel). The variant has been reported as Likely Benign by two clinical laboratories and Benign by one clinical laboratory.5 No functional studies, case-control data, segregation data, or co-occurrence observations involving this specific variant were identified in the literature. Publications reviewed (PMID 34242744, 15604628, 17508274, 18163131, 20301317) did not contain variant-specific evidence for NM_000051.3:c.5544T>C. Evidence summary: PM2_Supporting (1 pathogenic supporting) versus BP4_Supporting and BP7_Supporting (2 benign supporting). Under the CSPEC HBOP v1.5.0 combination rules, the presence of both pathogenic and benign supporting criteria triggers Rule 31, yielding a classification of Uncertain Significance — Conflicting Evidence.6

PM2 + BP4 + BP6 + BP7 VUS
Gene diagram · NM_000051.3 · variants mapped to exon structure
ATM NM_000051.3
Fetching transcript structure from UCSC…
Applied criteria · 4 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
      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= 6.19593e-07; MAF= 0.00006%, 1/1613962 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 1.33465e-05; MAF= 0.00133%, 1/74926 alleles, homozygotes = 0).
      v2.1
      This variant is present in gnomAD v2.1 (AF= 7.96794e-06; MAF= 0.00080%, 2/251006 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 6.15233e-05; MAF= 0.00615%, 1/16254 alleles, homozygotes = 0).
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      6.2e-05% · 1 / 1,613,962
      0 hom
      African/African American
      1 / 74,926
      0.0013%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, European (non-Finnish))
      gnomAD v2.1
      0.0008% · 2 / 251,006
      0 hom
      African/African American
      1 / 16,254
      0.0062%
      European (non-Finnish)
      1 / 113,420
      0.00088%
      + 6 not observed (Admixed American, 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 (2 clinical laboratories) and as Benign (1 clinical laboratory) and as Likely Benign by ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Variant Curation Expert Panel, ClinGen (expert panel). (ClinVarID = 184944)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.06).
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
      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
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 10 PMIDs not cited in assessment
      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
      20301790 ↗ PMID:20301790 CLINVAR
      24366376 ↗ Risk assessment, genetic counseling, and genetic testing for BRCA-related cancer in women: U.S. Preventive Services Task Force recommendation statement. 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