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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 applied · 9 assessed
Applied · 4
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
The variant is exceedingly rare in population databases: gnomAD v4.1 overall allele frequency is 6.20×10⁻⁷ (1/1,613,962 alleles, 0 homozygotes), which is ≤0.001%, satisfying the CSPEC HBOP PM2_Supporting frequency threshold. In gnomAD v2.1, AF is 7.97×10⁻⁶ (2/251,006 alleles, 0 homozygotes).
gnomAD v4.1: AF=6.20×10⁻⁷ (1/1613962 alleles
BP4 supporting Benign
SpliceAI predicts no significant splicing impact for this variant (maximum delta score = 0.06, which is ≤0.1), satisfying the CSPEC HBOP BP4_Supporting rule for no predicted splicing impact. REVEL is not applicable for this synonymous variant.
SpliceAI max delta = 0.06 (≤0.1 threshold)DS_AG=0.01DS_AL=0.06
BP6 supporting Benign
Expert panel ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Variant Curation Expert Panel, ClinGen classified as Likely benign.
ClinVar expert panel classification
BP7 supporting Benign
This is a synonymous variant (NP_000042.3:p.(Asp1848=)) located at c.5544 in exon 36 (c.5391–5562). The variant position is 18 nucleotides from the donor splice site (beyond the +7 boundary) and 153 nucleotides from the acceptor splice site (beyond the -21 boundary), satisfying the CSPEC HBOP BP7_Supporting definition for synonymous variants located outside donor/acceptor site boundaries. No RNA evidence for aberrant splicing exists to counter this assessment.
Synonymous variant NP_000042.3:p.(Asp1848=)Exon 36: c.5391–5562variant at c.5544
Assessed · not applied
Pathogenic
PS1 CSPEC HBOP PS1 applies to missense variants or splice-altering variants with a known (likely) pathogenic comparator at the same nucleotide.
PS3 No functional studies evaluating the impact of this specific synonymous variant on ATM protein function (phosphorylation of ATM-specific targets or radiosensitivity rescue) have been identified in the literature or functional databases.
PS4 No case-control studies evaluating this specific variant for enrichment in breast, ovarian, or pancreatic cancer cases versus controls have been identified.
PP1 No segregation data for this specific variant in families with ataxia-telangiectasia or cancer phenotypes has been identified.
PP3 This variant is synonymous, so the missense REVEL rule (>0.7333) is not applicable.
Benign
BA1 The CSPEC HBOP BA1 threshold requires Grpmax Filtering AF >0.5% in gnomAD v4.
BS1 The CSPEC HBOP BS1 threshold requires Grpmax Filtering AF >0.05% in gnomAD v4.
BS3 No functional studies evaluating whether this synonymous variant rescues ATM-specific features (phosphorylation of ATM-specific targets) and/or radiosensitivity have been identified.
BP2 No co-occurrence observations with known pathogenic ATM variants in unaffected (non-A-T) individuals are available to apply the CSPEC ATM PM3/BP2 point-based system for this specific variant.
N/A · 13 PVS1 · PS2 · PM1 · PM5 · PM6 · PP2 · PP4 · PP5 · BS2 · BS4 · BP1 · BP3 · BP5
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