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Variant interpretation report

ATM c.8174A>G, p.(Asp2725Gly)

NM_000051.3:c.8174A>G NP_000042.3:p.(Asp2725Gly) View identifiers
Classification
Uncertain significance

Variant description:

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.

In plain language

Gene-level background from the recorded interpretation.

About ATM

No gene-level summary was recorded for this case.

LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
01The reasoning

How it was classified

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.

Recorded applied criteria

The applied criteria and their strengths are shown as assessed under the stated framework.

Pathogenic evidence criteria: 2 Benign evidence criteria: 0
Pathogenic criteria applied · 2
PM2Supporting
PM2 · supporting

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.

PP3Supporting
PP3 · supporting

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.

Benign criteria applied · 0

No benign criterion marked as applied in the recorded assessment.

Recorded classification: Uncertain significance

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.

02The sources

Evidence at a glance

Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.

SpliceAI score
0.070 maximum delta

Recorded SpliceAI maximum delta score: 0.070. Refer to the recorded PP3/BP4 rationale for interpretation.

ClinVar submissions
3 reported laboratory submissions

3 Uncertain significance.

Context only ClinVar ↗
Functional evidence
Statement recorded

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.

No listed criterion applied OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
3 recorded samples

This variant has previously been reported in somatic cancers (COSMIC; COSV53728899, n = 3 times).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.

For specialists

Technical detail

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.

Met Not met Not assessed Not applicable

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.

Met · 2

PM2 SupportingThe 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. Details ▾Hide ▴
Evidence considered
  • gnomAD v4.1: 6/1
  • 613
  • 960 alleles
  • AF=0.00037%
  • grpmax FAF=0.00018%
  • all 6 alleles in European (non-Finnish) subpopulation
  • homozygotes=0. Absent from gnomAD v2.1 and gnomAD-Canada.
Sources
PP3 SupportingREVEL 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. Details ▾Hide ▴
Evidence considered
  • REVEL=0.968 (>0.7333 threshold)
  • SpliceAI max_delta=0.07 (no splicing concern)
  • VCEP supplement table classifies variant as Non-functional (Medium-high confidence) based on combined computational scores.
Sources
revelspliceai ↗vcep_suppl_tables1_pmid_40580951

Not met · 7 · evaluated, threshold not reached

PS1 No known pathogenic or likely pathogenic variant has been established at the same nucleotide position (c.8174). The ATM VCEP PS1 rule for missense changes requires a P or LP reference variant at the same residue with splicing ruled out for both. c.8174A>T (D2725V) is present in ClinVar as Uncertain significance and classified as Non-functional by the VCEP supplement table, thus does not serve as a P/LP comparator. Details ▾Hide ▴
Evidence considered
  • No P/LP variant at c.8174
  • the only alternate nucleotide change at this position (c.8174A>T) is ClinVar Uncertain significance and VCEP-classified Non-functional.
Sources
vcep_atm_ps1_1_5vcep_suppl_tables1_pmid_40580951
PS4 No case-control study has been identified that provides variant-specific odds ratio, relative risk, or p-value for NM_000051.3:c.8174A>G. The ATM VCEP requires p ≤ 0.05 AND (OR/HR/RR ≥ 2 OR lower 95% CI ≥ 1.5). The variant is absent from all reviewed publications at the variant level. Details ▾Hide ▴
Evidence considered
  • No case-control studies reporting variant-specific association statistics were identified among the 10 reviewed PMIDs.
Still missing
  • No variant-specific case-control data available.
Sources
PP5 No reputable source has reported NM_000051.3:c.8174A>G as pathogenic. The ClinGen HBOP VCEP lists PP5 as Not Applicable. Under generic ACMG/AMP, PP5 requires a reputable source to have recently reported the variant as pathogenic, which has not occurred for this variant. Details ▾Hide ▴
Evidence considered
  • ClinVar classification is Uncertain significance
  • no reputable source has reported this variant as pathogenic.
Sources
BA1 The grpmax filtering allele frequency in gnomAD v4.1 is 0.00018% (FAF=1.83e-06), which is well below the ATM VCEP BA1 threshold of >0.5%. Details ▾Hide ▴
Evidence considered
  • gnomAD v4.1 grpmax FAF=0.00018%
  • far below the 0.5% BA1 threshold.
Sources
BS1 The grpmax filtering allele frequency in gnomAD v4.1 is 0.00018% (FAF=1.83e-06), which is below the ATM VCEP BS1 threshold of >0.05%. Details ▾Hide ▴
Evidence considered
  • gnomAD v4.1 grpmax FAF=0.00018%
  • below the 0.05% BS1 threshold.
Sources
BP4 REVEL score of 0.968 exceeds the ATM VCEP BP4 missense threshold of ≤0.249. Multiple in silico predictors (REVEL 0.968, AlphaMissense 0.9984, BayesDel 0.482, boostDM 0.646, EVE 0.801) consistently suggest a deleterious effect. SpliceAI max delta score is 0.07, which is ≤0.1 for the splicing component of BP4, but this missense variant is assessed under the REVEL rule. Details ▾Hide ▴
Evidence considered
  • REVEL=0.968
  • far above the BP4 missense threshold of ≤0.249. Multiple independent in silico predictors concur on a deleterious prediction.
Sources
revelbayesdelspliceai ↗vcep_suppl_tables1_pmid_40580951
PS5 No reputable source has reported NM_000051.3:c.8174A>G as pathogenic. ClinVar lists this variant as Uncertain significance from three clinical laboratories. Under generic ACMG/AMP rules, PS5 requires a reputable source to report the variant as pathogenic with evidence unavailable for independent evaluation, which is not satisfied. Details ▾Hide ▴
Evidence considered
  • ClinVar classification is Uncertain significance (3 submitters)
  • no reputable source calls this variant pathogenic.
Sources

Not assessed · 4 · no assessment recorded

PS3 No variant-specific functional assay data have been reported for NM_000051.3:c.8174A>G. The ATM VCEP supplemental table (PMID:40580951) classifies this variant as Non-functional based on computational predictions (boostDM, EVE, REVEL, AlphaMissense), not experimental functional evidence. Color Health ClinVar submission (SCV000913075) explicitly states functional studies have not been reported for this variant. Details ▾Hide ▴
Evidence considered
  • Color Health ClinVar submission confirms no functional studies reported. VCEP supplement table classification is computational
  • not experimental.
Still missing
  • No experimental functional data (kinase activity assay
  • radiosensitivity assay
  • or other ATM functional readout) available for this variant.
Sources
clinvar ↗vcep_suppl_tables1_pmid_40580951
PP1 No segregation data are available for NM_000051.3:c.8174A>G. ATM-associated ataxia-telangiectasia is an autosomal recessive condition; the VCEP PP1 rule requires segregation in affected relatives. No family studies or cosegregation data involving this variant were identified in any reviewed source. Details ▾Hide ▴
Evidence considered
  • No segregation or family studies identified for this variant.
Still missing
  • No segregation data available.
BS3 No experimental functional studies demonstrating rescue of ATM function have been reported for NM_000051.3:c.8174A>G. The ATM VCEP BS3 rules require variant-specific experimental evidence showing rescue of ATM-specific features and/or radiosensitivity. No such data are available. Details ▾Hide ▴
Evidence considered
  • No experimental functional rescue data available for this variant.
Still missing
  • No experimental functional rescue data available.
Sources
BP2 No observations of NM_000051.3:c.8174A>G in trans with a pathogenic ATM variant in an unaffected individual were identified. The ATM VCEP BP2 rule requires co-occurrence data in unaffected (non-A-T) individuals, which were not found. Details ▾Hide ▴
Evidence considered
  • No trans-observation data available.
Still missing
  • No data on co-occurrence in trans with pathogenic ATM variants in unaffected individuals.
Not applicable · 13· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/ANM_000051.3:c.8174A>G is a missense variant (p.Asp2725Gly) and does not fall into the PVS1 null-variant buckets of nonsense, frameshift, or canonical ±1,2 splice consensus variants. The ATM VCEP PVS1 decision tree is not triggered. Details ▾Hide ▴
Evidence considered
  • Variant is a missense substitution
  • not a null variant
  • PVS1 is reserved for nonsense
  • frameshift
  • and canonical splice variants.
Sources
pvs1_variant_assessmentpvs1_gene_context
PS2 VCEPClinGen HBOP VCEP Version 1.5.0 lists PS2 as Not Applicable. Details ▾Hide ▴
Evidence considered
  • Criterion designated Not Applicable by the ClinGen HBOP VCEP for ATM.
Sources
PM1 VCEPClinGen HBOP VCEP Version 1.5.0 lists PM1 as Not Applicable. Details ▾Hide ▴
Evidence considered
  • Criterion designated Not Applicable by the ClinGen HBOP VCEP for ATM.
Sources
PM5 N/AThe ATM VCEP PM5 rule applies only to frameshifting or truncating variants with premature termination codons upstream of p.Arg3047, or splice variants meeting specific criteria. NM_000051.3:c.8174A>G is a missense variant (p.Asp2725Gly) and does not meet the VCEP PM5 structural requirements. Details ▾Hide ▴
Evidence considered
  • Variant is missense
  • VCEP PM5 is restricted to truncating/frameshift variants upstream of p.Arg3047 and qualifying splice variants.
Sources
cspec ↗pm5_candidates
PM6 VCEPClinGen HBOP VCEP Version 1.5.0 lists PM6 as Not Applicable. Details ▾Hide ▴
Evidence considered
  • Criterion designated Not Applicable by the ClinGen HBOP VCEP for ATM.
Sources
PP2 VCEPClinGen HBOP VCEP Version 1.5.0 lists PP2 as Not Applicable. Details ▾Hide ▴
Evidence considered
  • Criterion designated Not Applicable by the ClinGen HBOP VCEP for ATM.
Sources
PP4 VCEPClinGen HBOP VCEP Version 1.5.0 lists PP4 as Not Applicable. Details ▾Hide ▴
Evidence considered
  • Criterion designated Not Applicable by the ClinGen HBOP VCEP for ATM.
Sources
BS2 VCEPClinGen HBOP VCEP Version 1.5.0 lists BS2 as Not Applicable. Details ▾Hide ▴
Evidence considered
  • Criterion designated Not Applicable by the ClinGen HBOP VCEP for ATM.
Sources
BS4 VCEPClinGen HBOP VCEP Version 1.5.0 lists BS4 as Not Applicable. Details ▾Hide ▴
Evidence considered
  • Criterion designated Not Applicable by the ClinGen HBOP VCEP for ATM.
Sources
BP1 VCEPClinGen HBOP VCEP Version 1.5.0 lists BP1 as Not Applicable. Details ▾Hide ▴
Evidence considered
  • Criterion designated Not Applicable by the ClinGen HBOP VCEP for ATM.
Sources
BP5 VCEPClinGen HBOP VCEP Version 1.5.0 lists BP5 as Not Applicable. Details ▾Hide ▴
Evidence considered
  • Criterion designated Not Applicable by the ClinGen HBOP VCEP for ATM.
Sources
BP6 VCEPClinGen HBOP VCEP Version 1.5.0 lists BP6 as Not Applicable. Details ▾Hide ▴
Evidence considered
  • Criterion designated Not Applicable by the ClinGen HBOP VCEP for ATM.
Sources
BP7 N/ANM_000051.3:c.8174A>G is a missense variant (p.Asp2725Gly). The ATM VCEP BP7 rule applies to synonymous and deep intronic variants, not missense substitutions. No RNA-level evidence of normal splicing is available for BP7(RNA) consideration. Details ▾Hide ▴
Evidence considered
  • Variant is missense
  • BP7 is restricted to synonymous and deep intronic variants per VCEP specifications.
Sources

Identifiers

Gene
ATM
Transcript
NM_000051.3
Coding (HGVS c.)
NM_000051.3:c.8174A>G
Protein (HGVS p.)
NP_000042.3:p.(Asp2725Gly)
GRCh38
chr11:108335867 A>G
GRCh37
chr11:108206594 A>G
ClinVar
482631
COSMIC
COSV53728899

Gene diagram

Every interpreted variant in ATM, mapped onto the exon structure of NM_000051.3. Select a row to find it on the plot.

ATMNM_000051.3
Fetching transcript structure from UCSC…
gnomAD v4.1 6 / 1,613,960 alleles AF 3.72e-06 · 0 homozygotes · FAF 1.83e-06
gnomAD v2.1 Allele count data not recorded
gnomAD-Canada v1.0 Allele count data not recorded

By genetic ancestry

gnomAD v4.1

AF 3.7e-06 · 6 / 1,613,960 alleles · 0 hom · FAF 1.8e-06
European (non-Finnish)6 / 1,179,892 5.1e-06
0 alternate alleles recorded in 9 other groups: Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American.

Statements

gnomAD v4.1

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.

gnomAD v2.1

Absent from gnomAD v2.1.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

SpliceAI and Pangolin

SpliceAI acceptor lossat -22 bp
0.010
SpliceAI acceptor gainat +17 bp
0.070
SpliceAI donor lossat +94 bp
0.000
SpliceAI donor gainat -1 bp
0.000
Pangolin splice lossmagnitude shown
-0.040
Pangolin splice gain
0.030

Other predictors

REVEL
0.968
BayesDel
0.482

How the predictions were used

PP3 SupportingREVEL 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. Details ▾Hide ▴
Evidence considered
  • REVEL=0.968 (>0.7333 threshold)
  • SpliceAI max_delta=0.07 (no splicing concern)
  • VCEP supplement table classifies variant as Non-functional (Medium-high confidence) based on combined computational scores.
Sources
revelspliceai ↗vcep_suppl_tables1_pmid_40580951
BP4 REVEL score of 0.968 exceeds the ATM VCEP BP4 missense threshold of ≤0.249. Multiple in silico predictors (REVEL 0.968, AlphaMissense 0.9984, BayesDel 0.482, boostDM 0.646, EVE 0.801) consistently suggest a deleterious effect. SpliceAI max delta score is 0.07, which is ≤0.1 for the splicing component of BP4, but this missense variant is assessed under the REVEL rule. Details ▾Hide ▴
Evidence considered
  • REVEL=0.968
  • far above the BP4 missense threshold of ≤0.249. Multiple independent in silico predictors concur on a deleterious prediction.
Sources
revelbayesdelspliceai ↗vcep_suppl_tables1_pmid_40580951
BP7 N/ANM_000051.3:c.8174A>G is a missense variant (p.Asp2725Gly). The ATM VCEP BP7 rule applies to synonymous and deep intronic variants, not missense substitutions. No RNA-level evidence of normal splicing is available for BP7(RNA) consideration. Details ▾Hide ▴
Evidence considered
  • Variant is missense
  • BP7 is restricted to synonymous and deep intronic variants per VCEP specifications.
Sources

Statement

In silico

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.

Recorded publications

  • 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.
    Richards S et al. · 2015
    ACMG/AMP standards and guidelines for the interpretation of sequence variants. Provides the generic classification framework referenced by ATM VCEP. NM_000051.3:c.8174A>G is not mentioned in this paper.
    Does not name this variant
    PMID 25741868 ↗
  • Rare, protein-truncating variants in ATM, CHEK2 and PALB2, but not XRCC2, are associated with increased breast cancer risks.
    Decker B et al. · 2017
    Case-control study of rare protein-truncating variants in ATM, CHEK2, and PALB2 in breast cancer. Focuses on truncating variants; missense variant NM_000051.3:c.8174A>G was not identified in the full text.
    Does not name this variant
    PMID 28779002 ↗
  • Biallelic mutations in the ATM gene in T-prolymphocytic leukemia.
    Stilgenbauer S et al. · 1997
    Reports biallelic ATM mutations in T-prolymphocytic leukemia. Describes identification of ATM mutations in T-PLL patients but NM_000051.3:c.8174A>G was not identified in the abstract.
    Does not name this variant
    PMID 9334731 ↗
  • Hereditary Ataxia Overview.
    Adam MP et al. · 1993
    GeneReviews overview of hereditary ataxias. Provides general background on ataxia genetics; NM_000051.3:c.8174A>G is not mentioned.
    Does not name this variant
    PMID 20301317 ↗
  • Ataxia-Telangiectasia.
    Adam MP et al. · 1993
    GeneReviews entry on ataxia-telangiectasia. Provides clinical and genetic background on ATM-associated disease; NM_000051.3:c.8174A>G is not mentioned.
    Does not name this variant
    PMID 20301790 ↗
  • EFNS/ENS Consensus on the diagnosis and management of chronic ataxias in adulthood.
    van de Warrenburg BP et al. · 2014
    EFNS/ENS consensus guideline on the diagnosis and management of chronic ataxias in adulthood. Discusses genetic subtypes of ataxia at the gene level; NM_000051.3:c.8174A>G is not mentioned.
    Does not name this variant
    PMID 24418350 ↗
  • 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.
    Hampel H et al. · 2015
    ACMG/NSGC practice guideline on referral indications for cancer predisposition assessment. Provides clinical guidance on cancer genetics referral; NM_000051.3:c.8174A>G is not mentioned.
    Does not name this variant
    PMID 25394175 ↗
  • Breast Cancer Risk Genes - Association Analysis in More than 113,000 Women.
    Breast Cancer Association Consortium et al. · 2021
    Breast Cancer Association Consortium analysis of 34 putative breast cancer susceptibility genes in over 113,000 women. Reports gene-level associations for ATM; NM_000051.3:c.8174A>G was not identified in the abstract.
    Does not name this variant
    PMID 33471991 ↗
  • EFNS guidelines on the molecular diagnosis of ataxias and spastic paraplegias.
    Gasser T et al. · 2010
    EFNS guidelines on molecular diagnosis of ataxias and spastic paraplegias. Provides gene-level testing recommendations; NM_000051.3:c.8174A>G is not mentioned.
    Does not name this variant
    PMID 20050888 ↗

Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.

All source links

Statements for reports

The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.

gnomAD v4.1

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.

gnomAD v2.1

Absent from gnomAD v2.1.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

ClinVar

This variant has been reported in ClinVar as Uncertain significance (3 clinical laboratories). (ClinVarID = 482631)

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07). REVEL score = 0.968. BayesDel score = 0.482249.

Functional

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.

Somatic

This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV53728899, n = 3 times).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.