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Variant interpretation report

ATM c.103C>A, p.(Arg35=)

NM_000051.4:c.103C>A NP_000042.3:p.(Arg35=) View identifiers
Classification
Likely benign

Variant description:

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.

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. 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: 0 Benign evidence criteria: 3
Pathogenic criteria applied · 0

No pathogenic criterion marked as applied in the recorded assessment.

Benign criteria applied · 3
BS1Strong
BS1 · strong

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.

BP4Supporting
BP4 · supporting

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.

BP7Supporting
BP7 · supporting

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.

Recorded classification: Likely benign

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.

02The sources

Evidence at a glance

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

gnomAD v4.1
gnomAD v2.1
Population frequency
78 / 1,613,574 alleles

gnomAD v4.1: 78 / 1,613,574 alleles. Recorded AF 4.83399e-05. Recorded homozygote count 0.

gnomAD v2.1

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.

gnomAD-Canada

This variant is present in gnomAD-Canada v1.0 (AF= 0.00016290182450043442, 3/18416 alleles, homozygotes = 0).

SpliceAI score
0.000 maximum delta

Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.

ClinVar submissions
14 reported laboratory submissions

11 Likely benign · 3 Benign. ClinVar API review status: criteria provided, multiple submitters, no conflicts.

Context only ClinVar ↗
Functional evidence
Statement recorded

OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.

No listed criterion applied OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
No matching record reported

This variant has not previously been reported in somatic cancers (COSMIC).

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, 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.

Met Not met Not assessed Not applicable

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.

Met · 3

BS1 StrongVCEP 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. Details ▾Hide ▴
Evidence considered
  • gnomAD v4.1 grpmax FAF=0.00062571 (0.0626%) exceeds VCEP BS1 threshold of >0.05%. 78/1
  • 613
  • 574 alleles (AF=0.00483%)
  • homozygotes=0.
Sources
gnomad_v4 ↗cspec ↗vcep_suppl_tables1_pmid_40580951
BP4 SupportingVCEP 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. Details ▾Hide ▴
Evidence considered
  • SpliceAI delta=0.00
  • no predicted splicing impact. Synonymous variant deep in exon 3.
Sources
BP7 SupportingVCEP 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. Details ▾Hide ▴
Evidence considered
  • Synonymous variant in exon 3
  • c.103
  • distant from splice sites (+82 from donor
  • -30 from acceptor). SpliceAI delta=0.00.
Sources

Not met · 8 · evaluated, threshold not reached

PS3 No experimental functional studies exist for NM_000051.4:c.103C>A. VCEP ATM PS3 requires functional rescue assay data (failed rescue of ATM-specific feature and/or radiosensitivity), which is absent for this variant. The VCEP Supplementary Table S1 categorizes this variant as 'Functional' based on 'Computational prediction' only, not experimental evidence. Details ▾Hide ▴
Evidence considered
  • No functional assay data for this variant. Suppl Table S1 marks as Computational prediction only.
Still missing
  • No functional studies performed on this variant.
Sources
cspec ↗vcep_suppl_tables1_pmid_40580951
PS4 No case-control studies identified for NM_000051.4:c.103C>A. VCEP ATM PS4 requires case-control studies with p-value ≤0.05 and OR/HR/RR ≥2 or lower 95% CI ≥1.5. No such studies were found. Details ▾Hide ▴
Evidence considered
  • No case-control studies available for this variant.
Still missing
  • No case-control data.
Sources
PM2 VCEP ATM PM2 requires gnomAD v4 frequency ≤0.001%. Observed gnomAD v4.1 allele frequency is 4.83×10⁻⁵ (0.00483%; 78/1,613,574 alleles), which exceeds the 0.001% threshold. PM2 is not met. Details ▾Hide ▴
Evidence considered
  • gnomAD v4.1 AF=4.83e-05 (0.00483%) exceeds VCEP PM2 threshold of ≤0.001%.
Sources
PP1 No segregation data is available for NM_000051.4:c.103C>A. VCEP ATM PP1 requires segregation in affected relatives for autosomal recessive ataxia-telangiectasia. No family studies were identified. Details ▾Hide ▴
Evidence considered
  • No segregation data available.
Still missing
  • No family segregation studies.
Sources
PP3 VCEP ATM PP3 requires REVEL >0.733 for missense variants or SpliceAI ≥0.2 for splicing variants. NM_000051.4:c.103C>A is synonymous: no REVEL score available, and SpliceAI max delta is 0.00. Neither threshold is met. Details ▾Hide ▴
Evidence considered
  • SpliceAI delta=0.00 (below 0.2 threshold)
  • no REVEL score (synonymous variant).
Sources
spliceai ↗cspec ↗vcep_suppl_tables1_pmid_40580951
BA1 VCEP ATM BA1 requires grpmax filtering allele frequency >0.5% in gnomAD v4. Observed grpmax FAF in gnomAD v4.1 is 0.00062571 (0.0626%), well below the 0.5% threshold. BA1 is not met. Details ▾Hide ▴
Evidence considered
  • gnomAD v4.1 grpmax FAF=0.00062571 (0.0626%) below BA1 threshold of >0.5%.
Sources
BS3 No experimental functional data demonstrating rescue of ATM-specific features or radiosensitivity exists for NM_000051.4:c.103C>A. VCEP ATM BS3 requires functional rescue assays. The VCEP Supplementary Table S1 classifies this variant as 'Functional' based on 'Computational prediction' only, which does not constitute experimental rescue evidence. Details ▾Hide ▴
Evidence considered
  • No functional rescue assay data. Suppl Table S1 'Computational prediction' only.
Still missing
  • No experimental functional rescue studies.
Sources
cspec ↗vcep_suppl_tables1_pmid_40580951
BP2 No evidence of co-occurrence in trans with a pathogenic variant in ATM. VCEP ATM BP2 requires observation of the variant in trans with a pathogenic/likely pathogenic variant in unaffected (non-A-T) individuals, with point-based scoring per the PM3/BP2 table. No such data is available. Details ▾Hide ▴
Evidence considered
  • No co-occurrence in trans data available.
Still missing
  • No trans co-occurrence studies.
Sources
cspec ↗vcep_atm_pm3_bp2_1_5
Not applicable · 18· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/ASynonymous variant (p.Arg35=) does not fall into PVS1 null-variant buckets (nonsense, frameshift, canonical ±1,2 splice sites, initiation codon, or exon deletion). VCEP ATM PVS1 decision tree does not apply. Details ▾Hide ▴
Evidence considered
  • Synonymous substitution in exon 3
  • no null-variant mechanism.
Sources
pvs1_variant_assessmentpvs1_gene_contextcspec ↗
PS1 N/AVCEP ATM PS1 applies to missense changes with splicing ruled out, or splicing variants with comparable predictions. NM_000051.4:c.103C>A is a synonymous variant (p.Arg35=) with no amino acid change; no comparator missense or splicing variant to evaluate. Details ▾Hide ▴
Evidence considered
  • Synonymous variant
  • no amino acid change
  • PS1 not applicable.
Sources
cspec ↗vcep_atm_ps1_1_5
PS2 VCEPVCEP ATM marks PS2 as Not Applicable. Details ▾Hide ▴
Evidence considered
  • VCEP Not Applicable designation.
Sources
PM1 VCEPVCEP ATM marks PM1 as Not Applicable. Details ▾Hide ▴
Evidence considered
  • VCEP Not Applicable designation.
Sources
PM3 N/ASkipped per instruction: not in assess list for this case. Details ▾Hide ▴

No further detail was recorded.

PM4 N/ASkipped per instruction: non-repeat indels and stop-loss only. Details ▾Hide ▴

No further detail was recorded.

PM5 N/AVCEP ATM PM5 applies only to frameshifting or truncating variants with premature termination codons upstream of p.Arg3047, and to splice variants with NMD-prone PTCs where PVS1_VS(RNA) is applied. NM_000051.4:c.103C>A is a synonymous variant and does not meet these criteria. Details ▾Hide ▴
Evidence considered
  • Synonymous variant
  • not frameshifting
  • truncating
  • or splicing
  • PM5 not applicable.
Sources
cspec ↗pm5_candidates
PM6 VCEPVCEP ATM marks PM6 as Not Applicable. Details ▾Hide ▴
Evidence considered
  • VCEP Not Applicable designation.
Sources
PP2 VCEPVCEP ATM marks PP2 as Not Applicable. Details ▾Hide ▴
Evidence considered
  • VCEP Not Applicable designation.
Sources
PP4 VCEPVCEP ATM marks PP4 as Not Applicable. Details ▾Hide ▴
Evidence considered
  • VCEP Not Applicable designation.
Sources
PP5 VCEPVCEP ATM marks PP5 as Not Applicable. Details ▾Hide ▴
Evidence considered
  • VCEP Not Applicable designation.
Sources
BS2 VCEPVCEP ATM marks BS2 as Not Applicable. Details ▾Hide ▴
Evidence considered
  • VCEP Not Applicable designation.
Sources
BS4 VCEPVCEP ATM marks BS4 as Not Applicable. Details ▾Hide ▴
Evidence considered
  • VCEP Not Applicable designation.
Sources
BP1 VCEPVCEP ATM marks BP1 as Not Applicable. Details ▾Hide ▴
Evidence considered
  • VCEP Not Applicable designation.
Sources
BP3 VCEPSkipped per instruction: in-frame indels only; substitution variant. Details ▾Hide ▴

No further detail was recorded.

BP5 VCEPVCEP ATM marks BP5 as Not Applicable. Details ▾Hide ▴
Evidence considered
  • VCEP Not Applicable designation.
Sources
BP6 VCEPVCEP ATM marks BP6 as Not Applicable. Details ▾Hide ▴
Evidence considered
  • VCEP Not Applicable designation.
Sources
PS5 N/APS5 is not defined in the VCEP ATM framework. No applicable VCEP rule exists for this criterion. Details ▾Hide ▴
Evidence considered
  • Not in VCEP ATM criteria set.
Sources

Identifiers

Gene
ATM
Transcript
NM_000051.4
Coding (HGVS c.)
NM_000051.4:c.103C>A
Protein (HGVS p.)
NP_000042.3:p.(Arg35=)
GRCh38
chr11:108227806 C>A
GRCh37
chr11:108098533 C>A
ClinVar
183805

Gene diagram

Every interpreted variant in ATM, mapped onto the exon structure of NM_000051.4. Select a row to find it on the plot.

ATMNM_000051.4
Fetching transcript structure from UCSC…
gnomAD v4.1 78 / 1,613,574 alleles AF 4.83e-05 · 0 homozygotes · FAF 0.000626
gnomAD v2.1 28 / 282,600 alleles AF 9.91e-05 · 0 homozygotes · FAF 0.000539
gnomAD-Canada v1.0 Allele count data not recorded

By genetic ancestry

gnomAD v4.1

AF 4.8e-05 · 78 / 1,613,574 alleles · 0 hom · FAF 0.00063
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
0 alternate alleles recorded in 6 other groups: European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish.

gnomAD v2.1

AF 9.9e-05 · 28 / 282,600 alleles · 0 hom · FAF 0.00054
African/African American22 / 24,868 0.00088
Admixed American5 / 35,424 0.00014
Remaining individuals1 / 7,206 0.00014
0 alternate alleles recorded in 5 other groups: Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), South Asian.

gnomAD-Canada

AF not recorded · ? / ? alleles

Statements

gnomAD v4.1

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.

gnomAD v2.1

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.

gnomAD-Canada

This variant is present in gnomAD-Canada v1.0 (AF= 0.00016290182450043442, 3/18416 alleles, homozygotes = 0).

Open the gnomAD-Canada detail page →

SpliceAI and Pangolin

Pangolin splice lossmagnitude shown
-0.010
Pangolin splice gain
0.070

Other predictors

REVEL
Not available
BayesDel
Not available

How the predictions were used

BP4 SupportingVCEP 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. Details ▾Hide ▴
Evidence considered
  • SpliceAI delta=0.00
  • no predicted splicing impact. Synonymous variant deep in exon 3.
Sources
BP7 SupportingVCEP 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. Details ▾Hide ▴
Evidence considered
  • Synonymous variant in exon 3
  • c.103
  • distant from splice sites (+82 from donor
  • -30 from acceptor). SpliceAI delta=0.00.
Sources
PP3 VCEP ATM PP3 requires REVEL >0.733 for missense variants or SpliceAI ≥0.2 for splicing variants. NM_000051.4:c.103C>A is synonymous: no REVEL score available, and SpliceAI max delta is 0.00. Neither threshold is met. Details ▾Hide ▴
Evidence considered
  • SpliceAI delta=0.00 (below 0.2 threshold)
  • no REVEL score (synonymous variant).
Sources
spliceai ↗cspec ↗vcep_suppl_tables1_pmid_40580951

Statement

In silico

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.

Recorded publications

  • Radiation exposure, the ATM Gene, and contralateral breast cancer in the women's environmental cancer and radiation epidemiology study.
    Bernstein JL et al. · 2010
    Studied ATM variants in relation to radiation exposure and contralateral breast cancer risk. NM_000051.4:c.103C>A was not identified in the abstract.
    Does not name this variant
    PMID 20305132 ↗
  • Tamoxifen and risk of contralateral breast cancer for BRCA1 and BRCA2 mutation carriers.
    Examined tamoxifen and contralateral breast cancer risk in BRCA1/BRCA2 mutation carriers. NM_000051.4:c.103C>A was not identified in the abstract.
    Does not name this variant
    PMID 23918944 ↗
  • 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. General framework document; NM_000051.4:c.103C>A was not mentioned in this paper.
    Does not name this variant
    PMID 25741868 ↗
  • ATM gene alterations in childhood acute lymphoblastic leukemias.
    Gumy Pause F et al. · 2003
    Investigated ATM gene alterations in childhood acute lymphoblastic leukemias. NM_000051.4:c.103C>A was not identified in this paper.
    Does not name this variant
    PMID 12673804 ↗
  • Risk assessment and genetic counseling for hereditary breast and ovarian cancer: recommendations of the National Society of Genetic Counselors.
    National Society of Genetic Counselors practice guidelines for hereditary breast and ovarian cancer risk assessment and genetic counseling. NM_000051.4:c.103C>A was not identified in the abstract.
    Does not name this variant
    PMID 17508274 ↗
  • The emerging landscape of breast cancer susceptibility.
    Stratton MR et al. · 2008
    Review of breast cancer susceptibility genes and their clinical implications. NM_000051.4:c.103C>A was not identified in the abstract.
    Does not name this variant
    PMID 18163131 ↗
  • BRCA1- and BRCA2-Associated Hereditary Breast and Ovarian Cancer.
    Adam MP et al. · 1993
    GeneReviews entry for BRCA1- and BRCA2-associated hereditary breast and ovarian cancer. NM_000051.4:c.103C>A was not identified.
    Does not name this variant
    PMID 20301425 ↗
  • American Society of Clinical Oncology Expert Statement: collection and use of a cancer family history for oncology providers.
    ASCO expert statement on collection and use of cancer family history. NM_000051.4:c.103C>A was not identified.
    Does not name this variant
    PMID 24493721 ↗
  • Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
    Sherloc comprehensive refinement of ACMG-AMP variant classification criteria. NM_000051.4:c.103C>A was not identified.
    Does not name this variant
    PMID 28492532 ↗

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= 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.

gnomAD v2.1

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.

gnomAD-Canada

This variant is present in gnomAD-Canada v1.0 (AF= 0.00016290182450043442, 3/18416 alleles, homozygotes = 0).

ClinVar

This variant has been reported in ClinVar as Likely benign (11 clinical laboratories) and as Benign (3 clinical laboratories). (ClinVarID = 183805)

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).

Functional

OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.

Somatic

This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.