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ATM
Final classification
Likely Benign
ATM c.7974T>C · p.Asn2658=
ATM

NM_000051.4:c.7974T>C is a synonymous variant p.(Asn2658=) in ATM exon 54, located well outside the canonical splice consensus regions.

Gene
ATM
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.7974T>C
Consequence
N/A
GRCh38
chr11:108333932 T>C
GRCh37
chr11:108204659 T>C
Basis Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework: matched Rule19 (Benign.Supporting >=2) with applied criteria: PM2 supporting, 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: PM2 supporting, BP4 supporting, BP7 supporting; maps to Likely Benign.
Classification rationale
PM2 BP4BP7 Likely Benign
ATM c.7974T>C

NM_000051.4:c.7974T>C is a synonymous variant p.(Asn2658=) in ATM exon 54, located well outside the canonical splice consensus regions. SpliceAI predicts no splice impact (max delta score = 0.00).1 This variant is present in gnomAD v4.1 at very low frequency (total AF = 0.00031%, 5/1,611,834 alleles, 0 homozygotes), highest in East Asian population (sub-population AF = 0.011%).2 ClinVar reports this variant as Likely benign (4 clinical laboratories) and Benign (1 laboratory); review status: criteria provided, single submitter (ClinVar Variation ID: 414583).3 The ClinGen HBOP VCEP supplementary table (PMID:40580951, Table S1) classifies this variant as Likely benign with an eDA score of 3.10e-06.4 BP7_Supporting is met: synonymous variant outside donor +7 and acceptor -21 splice regions with no predicted splice impact (SpliceAI = 0.0).5 BP4_Supporting is met: no predicted impact via splicing (SpliceAI max delta = 0.0 ≤ 0.1). Note partial overlap with BP7.6 PM2_Supporting is met: gnomAD v4.1 total allele frequency (0.00031%) is ≤ 0.001% VCEP threshold. Per VCEP guidance, PM2 is not considered conflicting evidence for variants that otherwise are likely benign/benign.7 No pathogenic criteria beyond PM2_Supporting are met. Multiple benign supporting criteria (BP7, BP4) are met with no conflicting pathogenic evidence per VCEP PM2 guidance.8 The ClinGen HBOP Expert Panel classification from the VCEP supplementary table is Likely benign, which is concordant with the evidence-based assessment.9

PM2 + BP4 + BP7 Likely Benign
4 vcep_suppl_tables1_pmid_40580951
9 vcep_suppl_tables1_pmid_40580951
Gene diagram · NM_000051.4 · variants mapped to exon structure
ATM NM_000051.4
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 9 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is present at very low frequency in gnomAD v4.1 (total AF = 0.00031%, 5/1,611,834 alleles, 0 homozygotes), meeting the VCEP PM2_Supporting threshold of ≤0.001%. Observed predominantly in the East Asian population (sub-population AF = 0.011%). Per VCEP guidance, PM2 is not considered conflicting evidence for variants that otherwise are likely benign/benign.
gnomAD v4.1 total AF = 0.00031% (≤0.001% threshold).VCEP PM2 is downgraded to Supporting strength only.
BP4 supporting Benign
SpliceAI predicts no splice impact (max delta = 0.0), meeting the VCEP BP4 threshold of SpliceAI ≤0.1 for splicing prediction. Multiple lines of computational evidence (SpliceAI) suggest no impact on splicing. REVEL not available for synonymous variants. Note: BP4 and BP7 both draw from the same underlying observation of absent splice impact; applied together they may overlap.
SpliceAI max delta = 0.0 (≤ 0.1 BP4 threshold).No predicted splice impact.
BP7 supporting Benign
NM_000051.4:c.7974T>C is a synonymous variant p.(Asn2658=) located in exon 54 (c.7939-c.8077). The variant is 35 nucleotides downstream of the acceptor site and 103 nucleotides upstream of the donor site, placing it well outside the VCEP-defined splice consensus regions (+7 donor, -21 acceptor). SpliceAI predicts no splice impact (max delta = 0.0). VCEP BP7 criteria for synonymous variants are met.
Synonymous variant outside donor +7 and acceptor -21.SpliceAI max delta = 0.0 (no predicted splice impact).VCEP BP7_Supporting criteria satisfied.
Assessed · not applied
Pathogenic
PS3 No well-established in vitro or in vivo functional studies identified for this variant.
PS4 No case-control studies demonstrating statistically significant enrichment of this variant in affected individuals versus controls are available.
PP1 No co-segregation data available for this variant.
PP3 SpliceAI predicts no splice impact (max delta = 0.0), failing the VCEP PP3 threshold of SpliceAI ≥0.2 for silent variants.
PP5 The ClinGen HBOP VCEP supplementary table (PMID:40580951) classifies this variant as Likely benign.
Benign
BA1 gnomAD v4.1 grpmax filtering AF = 0.00435%, which does not exceed the VCEP BA1 threshold of >0.5%.
BS1 gnomAD v4.1 grpmax filtering AF = 0.00435%, which does not exceed the VCEP BS1 threshold of >0.05%.
BS3 No well-established in vitro or in vivo functional studies demonstrating normal protein function or splicing for this variant.
BP2 No evidence of this variant observed in trans with a pathogenic ATM variant in unaffected individuals (≥18 years, no A-T).
N/A · 13 PVS1 · PS1 · PS2 · PM1 · PM5 · PM6 · PP2 · PP4 · BS2 · BS4 · BP1 · 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= 3.10206e-06; MAF= 0.00031%, 5/1611834 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 0.000111418; MAF= 0.01114%, 5/44876 alleles, homozygotes = 0); grpmax FAF= 4.346e-05.
v2.1
This variant is present in gnomAD v2.1 (AF= 2.38796e-05; MAF= 0.00239%, 6/251260 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 0.000326193; MAF= 0.03262%, 6/18394 alleles, homozygotes = 0); grpmax FAF= 0.00014146.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00031% · 5 / 1,611,834
0 hom · FAF 0.0043%
East Asian
5 / 44,876
0.011%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish))
gnomAD v2.1
0.0024% · 6 / 251,260
0 hom · FAF 0.014%
East Asian
6 / 18,394
0.033%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, European (Finnish), European (non-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 = 414583)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
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
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
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
24432435 ↗ PMID 24432435 CLINVAR
26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Versi CLINVAR
31429903 ↗ Risk Assessment, Genetic Counseling, and Genetic Testing for BRCA-Related Cancer: US Preventive Services Task Force Recommendation Statement. CLINVAR
35802134 ↗ ACMG SF v3.1 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
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