About ATM
No gene-level summary was recorded for this case.
No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is likely benign. Select a step to read what it means.
Likely benign.A likely benign classification under the recorded framework.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.No gene-level summary was recorded for this case.
The recorded framework is ClinGen ATM VCEP v1.5. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
The applied criteria and their strengths are shown as assessed under the stated framework.
No pathogenic criterion marked as applied in the recorded assessment.
VCEP ATM BS1 requires grpmax filtering allele frequency >0.05% in gnomAD v4. Observed grpmax FAF in gnomAD v4.1 is 0.00062571 (0.0626%), exceeding the 0.05% threshold. The variant is present in 78 of 1,613,574 alleles in gnomAD v4.1 with highest subpopulation frequency in African/African American (AF=0.0787%). BS1 is met at Strong strength.
VCEP ATM BP4 for splicing: no predicted impact via splicing (SpliceAI ≤0.1). SpliceAI max delta score is 0.00 for NM_000051.4:c.103C>A, indicating no predicted splicing alteration. The variant is deep within exon 3 (82 bases from donor site, 30 bases from acceptor site). BP4 is met at Supporting strength.
VCEP ATM BP7 applies to synonymous variants located further than +7 from the donor site and further than -21 from the acceptor site. NM_000051.4:c.103C>A is a synonymous variant (p.Arg35=) in exon 3 (c.73-185), positioned 82 bases upstream of the donor site and 30 bases downstream of the acceptor site, well outside the splice consensus regions. SpliceAI delta is 0.00, confirming no predicted splicing impact. BP7 is met at Supporting strength.
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 Rule19 (Benign.Supporting >=2) with applied criteria: BS1 strong benign, BP4 supporting benign, BP7 supporting benign; maps to Likely Benign.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 78 / 1,613,574 alleles. Recorded AF 4.83399e-05. Recorded homozygote count 0.
This variant is present in gnomAD v2.1 (AF= 9.908e-05; MAF= 0.00991%, 28/282600 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000884671; MAF= 0.08847%, 22/24868 alleles, homozygotes = 0); grpmax FAF= 0.00053895.
This variant is present in gnomAD-Canada v1.0 (AF= 0.00016290182450043442, 3/18416 alleles, homozygotes = 0).
Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.
11 Likely benign · 3 Benign. ClinVar API review status: criteria provided, multiple submitters, no conflicts.
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.
ACMG/AMP criteria under ClinGen ATM VCEP v1.5, with the data and sources behind each one.
29 criteria with recorded statuses: 3 met · 8 not met · 0 not assessed · 18 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
NM_000051.4:c.103C>A (p.Arg35=) is a synonymous variant in exon 3 of ATM.
This variant is present in gnomAD v4.1 at an allele frequency of 0.00483% (78/1,613,574 alleles) with a grpmax filtering allele frequency of 0.0626% in the African/African American population, exceeding the VCEP ATM BS1 threshold of >0.05% (BS1_Strong).
SpliceAI predicts no splicing impact (max delta = 0.00), supporting a benign interpretation (BP4_Supporting).
The variant is a synonymous substitution deep within exon 3, located 82 bases from the donor site and 30 bases from the acceptor site, well outside splice consensus regions. No aberrant splicing is predicted (BP7_Supporting).
The VCEP ATM ClinGen HBOP Supplementary Table S1 (PMID 40580951) classifies this variant as Benign/Likely benign based on computational prediction, consistent with the criteria assessment.
Classification: Likely Benign per VCEP ATM Rule 18 (1 Strong benign + ≥1 Supporting benign). BS1_Strong, BP4_Supporting, and BP7_Supporting are met. No pathogenic criteria are met.
No criteria match.
No further detail was recorded.
No further detail was recorded.
No further detail was recorded.
Every interpreted variant in ATM, mapped onto the exon structure of NM_000051.4. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
| African/African American59 / 74,976 | 0.00079 |
| Admixed American10 / 59,996 | 0.00017 |
| Remaining individuals5 / 62,478 | 8e-05 |
| European (non-Finnish)4 / 1,179,806 | 3.4e-06 |
| African/African American22 / 24,868 | 0.00088 |
| Admixed American5 / 35,424 | 0.00014 |
| Remaining individuals1 / 7,206 | 0.00014 |
This variant is present in gnomAD v4.1 (AF= 4.83399e-05; MAF= 0.00483%, 78/1613574 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000786918; MAF= 0.07869%, 59/74976 alleles, homozygotes = 0); grpmax FAF= 0.00062571.
This variant is present in gnomAD v2.1 (AF= 9.908e-05; MAF= 0.00991%, 28/282600 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000884671; MAF= 0.08847%, 22/24868 alleles, homozygotes = 0); grpmax FAF= 0.00053895.
This variant is present in gnomAD-Canada v1.0 (AF= 0.00016290182450043442, 3/18416 alleles, homozygotes = 0).
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
9 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
This variant is present in gnomAD v4.1 (AF= 4.83399e-05; MAF= 0.00483%, 78/1613574 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000786918; MAF= 0.07869%, 59/74976 alleles, homozygotes = 0); grpmax FAF= 0.00062571.
This variant is present in gnomAD v2.1 (AF= 9.908e-05; MAF= 0.00991%, 28/282600 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000884671; MAF= 0.08847%, 22/24868 alleles, homozygotes = 0); grpmax FAF= 0.00053895.
This variant is present in gnomAD-Canada v1.0 (AF= 0.00016290182450043442, 3/18416 alleles, homozygotes = 0).
This variant has been reported in ClinVar as Likely benign (11 clinical laboratories) and as Benign (3 clinical laboratories). (ClinVarID = 183805)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.