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
Uncertain Significance - Conflicting Evidence
ATM c.7835G>A · p.Arg2612Lys
ATM

NM_000051.4:c.7835G>A (p.Arg2612Lys) is a missense variant in ATM, a gene where loss of function is an established mechanism for ataxia telangiectasia (autosomal recessive) and ATM-related cancer predisposition (autosomal dominant). The variant is absent from gnomAD v4.1 and present at extremely low frequency in gnomAD v2.1 (1/250,772 alleles, NFE only).

Gene
ATM
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.7835G>A
Consequence
N/A
GRCh38
chr11:108332808 G>A
GRCh37
chr11:108203535 G>A
Basis ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for ATM Version 1.5 v1.5 criteria-combination framework: matched Rule31 (Benign.Supporting >=1 + Pathogenic.Supporting >=1) with applied criteria: PM2 supporting, BP4 supporting benign; maps to Uncertain Significance - Conflicting Evidence.
ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for ATM Version 1.5 v1.5 criteria-combination framework: matched Rule31 (Benign.Supporting >=1 + Pathogenic.Supporting >=1) with applied criteria: PM2 supporting, BP4 supporting benign; maps to Uncertain Significance - Conflicting Evidence.
Classification rationale
PM2 BP4 Uncertain Significance - Conflicting Evidence
ATM c.7835G>A

NM_000051.4:c.7835G>A (p.Arg2612Lys) is a missense variant in ATM, a gene where loss of function is an established mechanism for ataxia telangiectasia (autosomal recessive) and ATM-related cancer predisposition (autosomal dominant). The variant is absent from gnomAD v4.1 and present at extremely low frequency in gnomAD v2.1 (1/250,772 alleles, NFE only).1 PM2_Supporting is met: the variant frequency (absent from gnomAD v4.1) satisfies the VCEP threshold of ≤0.001%.2 BP4_Supporting is met: REVEL score of 0.086 is ≤0.249, SpliceAI max delta of 0.0 is ≤0.1, and BayesDel score of −0.523 is in the benign range. Multiple computational tools consistently predict a neutral effect.3 No functional data (PS3/BS3), segregation data (PP1), case-control data (PS4), or variant-specific publications were identified for this variant. OncoKB reports unknown oncogenic effect, and the VCEP supplementary functional tables do not include p.Arg2612Lys.4 This variant has been reported in ClinVar as Uncertain significance by two clinical laboratories and as Likely benign by one clinical laboratory (Variation ID 407542). No expert panel classification is available.5 Under the ClinGen HBOP ATM VCEP v1.5 combination rules, PM2_Supporting (1 pathogenic supporting) and BP4_Supporting (1 benign supporting) together trigger Rule 31: Uncertain Significance — Conflicting Evidence.6

PM2 + BP4 Uncertain Significance - Conflicting Evidence
3 revelspliceai ↗bayesdelcspec ↗
4 oncokb ↗vcep_suppl_tables1_pmid_40580951vcep_clingen_hbop_atm_supplementary_tables_1_and_2_v1
Gene diagram · NM_000051.4 · variants mapped to exon structure
ATM NM_000051.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 9 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is absent from gnomAD v4.1. Under the ATM VCEP PM2 rule, a frequency ≤0.001% in gnomAD v4 qualifies for PM2_Supporting. In gnomAD v2.1, the variant is present at extremely low frequency (AF=3.99×10⁻⁶; 1/250,772 alleles, NFE subpopulation only, no homozygotes).
Absent from gnomAD v4.1. gnomAD v2.1: 1/250772 alleles (AF=3.99×10⁻⁶)single NFE heterozygote. VCEP threshold ≤0.001% satisfied.
BP4 supporting Benign
REVEL score is 0.086, which is ≤0.249 (VCEP BP4 threshold for missense variants). SpliceAI predicts no splicing impact (max delta = 0.0, which is ≤0.1). BayesDel score is −0.523 (predicted benign). Multiple independent computational tools consistently predict a neutral effect on the gene product.
REVEL: 0.086 (threshold ≤0.249). SpliceAI: max delta = 0.0 (threshold ≤0.1). BayesDel: −0.523 (predicted benign).
Assessed · not applied
Pathogenic
PS1 No evidence that the same amino acid change (p.Arg2612Lys) produced by a different nucleotide substitution has been classified as pathogenic or likely pathogenic.
PS3 No functional data available for NM_000051.4:c.7835G>A (p.Arg2612Lys).
PS4 No case-control studies or affected individual case reports featuring NM_000051.4:c.7835G>A were identified.
PP1 No segregation data are available for this variant.
PP3 REVEL score is 0.086, which is well below the VCEP PP3 threshold of >0.7333 for missense variants.
Benign
BA1 The variant is absent from gnomAD v4.1.
BS1 The variant is absent from gnomAD v4.1.
BS3 No functional data demonstrating a benign effect for NM_000051.4:c.7835G>A (p.Arg2612Lys) are available.
BP2 No evidence that this variant has been observed in trans with a pathogenic or likely pathogenic ATM variant in an unaffected individual aged 18 years or older.
N/A · 17 PVS1 · PS2 · PM1 · PM3 · PM4 · PM5 · PM6 · PP2 · PP4 · PP5 · BS2 · BS4 · BP1 · BP3 · BP5 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
This variant is present in gnomAD v2.1 (AF= 3.98769e-06; MAF= 0.00040%, 1/250772 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.82441e-06; MAF= 0.00088%, 1/113322 alleles, homozygotes = 0).
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
0.0004% · 1 / 250,772
0 hom
European (non-Finnish)
1 / 113,322
0.00088%
+ 7 not observed (African/African American, 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 Uncertain significance (2 clinical laboratories) and as Likely benign (1 clinical laboratory). (ClinVarID = 407542)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.086. BayesDel score = -0.523282.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. ATM, a kinase involved in the DNA damage response, is mutated in various solid and hematologic malignancies.
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 · 5 PMIDs not cited in assessment
20301317 ↗ Hereditary Ataxia Overview. CLINVAR
20301790 ↗ Ataxia-Telangiectasia. CLINVAR
24418350 ↗ EFNS/ENS Consensus on the diagnosis and management of chronic ataxias in adulthood. CLINVAR
25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
20050888 ↗ EFNS guidelines on the molecular diagnosis of ataxias and spastic paraplegias. CLINVAR