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 uncertain. Select a step to read what it means.
Uncertain.The recorded classification is uncertain significance.
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 v1.5.0. 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.
The variant frequency in gnomAD v4.1 (AF=0.00037%, 6/1,613,960 alleles; grpmax FAF=0.00018%) is ≤0.001% per the ATM VCEP PM2 rule. The variant is absent from gnomAD v2.1 and gnomAD-Canada. At 0.00037%, this meets the VCEP PM2_Supporting threshold.
REVEL score of 0.968 exceeds the ATM VCEP PP3 threshold of >0.7333 for missense variants. SpliceAI predicts no significant splice impact (max delta=0.07). The VCEP supplemental table (PMID:40580951) independently classifies this variant as Non-functional based on a combined computational score integrating boostDM, EVE, REVEL, and AlphaMissense, consistent with a deleterious in silico prediction.
No benign criterion marked as applied in the recorded assessment.
Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting, PP3 supporting; no rule matched the adjudicated criteria.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 6 / 1,613,960 alleles. Recorded AF 3.71756e-06. Recorded homozygote count 0.
Absent from gnomAD v2.1.
Absent from gnomAD-Canada v1.0.
Recorded SpliceAI maximum delta score: 0.070. Refer to the recorded PP3/BP4 rationale for interpretation.
3 Uncertain significance.
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.
This variant has previously been reported in somatic cancers (COSMIC; COSV53728899, n = 3 times).
This variant does not lie in a statistically significant hotspot.
ACMG/AMP criteria under ClinGen ATM VCEP v1.5.0, with the data and sources behind each one.
26 criteria with recorded statuses: 2 met · 7 not met · 4 not assessed · 13 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
NM_000051.3:c.8174A>G (p.Asp2725Gly) in ATM is a rare missense variant observed in gnomAD v4.1 at a frequency of 0.00037% (6/1,613,960 alleles), meeting ATM VCEP PM2_Supporting.
In silico prediction tools consistently suggest a deleterious effect: REVEL score of 0.968 exceeds the ATM VCEP PP3_Supporting threshold of >0.7333, and the ClinGen HBOP VCEP supplemental table classifies this variant as Non-functional with Medium-high confidence based on combined computational scores.
No functional studies, segregation data, case-control analyses, or trans-observation data are available for this variant. The variant has not been reported as pathogenic by any reputable source.
With PM2_Supporting and PP3_Supporting as the only met criteria, this variant does not reach the threshold for Likely Pathogenic or Likely Benign under the ClinGen HBOP VCEP v1.5.0 combination rules. The classification is Uncertain Significance.
No criteria match.
Every interpreted variant in ATM, mapped onto the exon structure of NM_000051.3. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
| European (non-Finnish)6 / 1,179,892 | 5.1e-06 |
This variant is present in gnomAD v4.1 (AF= 3.71756e-06; MAF= 0.00037%, 6/1613960 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 5.08521e-06; MAF= 0.00051%, 6/1179892 alleles, homozygotes = 0); grpmax FAF= 1.83e-06.
Absent from gnomAD v2.1.
Absent from gnomAD-Canada v1.0.
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07). REVEL score = 0.968. BayesDel score = 0.482249.
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= 3.71756e-06; MAF= 0.00037%, 6/1613960 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 5.08521e-06; MAF= 0.00051%, 6/1179892 alleles, homozygotes = 0); grpmax FAF= 1.83e-06.
Absent from gnomAD v2.1.
Absent from gnomAD-Canada v1.0.
This variant has been reported in ClinVar as Uncertain significance (3 clinical laboratories). (ClinVarID = 482631)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07). REVEL score = 0.968. BayesDel score = 0.482249.
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.
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV53728899, n = 3 times).
This variant does not lie in a statistically significant hotspot.