0%
ATMc.6897C>TLikely benign
Print report
Variant interpretation report

ATM c.6897C>T, p.(Phe2299=)

NM_000051.4:c.6897C>T NP_000042.3:p.(Phe2299=) Synonymous · exon 47 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

ATM encodes a kinase that acts as a master controller of the cellular DNA damage response: it detects double-strand breaks and coordinates DNA repair, cell cycle arrest, or apoptosis through downstream targets including p53, BRCA1, and CHK2. Loss-of-function mutations in both copies of ATM cause ataxia telangiectasia, an autosomal recessive disorder characterized by neurological problems, immune deficiency, and cancer predisposition. ATM functions as a tumor suppressor: individuals with ataxia telangiectasia are prone to childhood lymphomas, leukemias, and breast cancer, while carriers of a single altered copy have increased risk of breast, pancreatic, prostate, and other cancers. Somatic ATM mutations also occur in lymphoid malignancies and solid tumors, and ATM-deficient cancers are often especially sensitive to DNA-damaging treatments.

NCBI Gene ↗ OncoKB ↗
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 v1.6. 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
BS3Supporting
BS3 · supporting

Met at Supporting: direct prime-editing classified c.6897C>T as Functional with High confidence and DeepATM_predicted=No.

BP4Supporting
BP4 · supporting

Met: SpliceAI maximum delta score 0.009 is at or below the VCEP BP4 threshold of 0.1.

BP7Supporting
BP7 · supporting

Met: The variant is synonymous (p.Phe2299=), which is explicitly within the VCEP BP7 supporting scope.

Recorded classification: Likely benign

Likely Benign: BS3, BP4, and BP7, each at supporting strength, satisfy the ATM VCEP Rule19 requirement of at least two benign supporting criteria.

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
33 / 1,613,946 alleles

gnomAD v4.1: 33 / 1,613,946 alleles. Recorded AF 2.04468e-05. Recorded homozygote count 0.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 1.59175e-05; MAF= 0.00159%, 4/251296 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.52051e-05; MAF= 0.00352%, 4/113620 alleles, homozygotes = 0); grpmax FAF= 1.122e-05.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

No listed criterion applied
gnomAD v4.1 ↗gnomAD v2.1 ↗gnomAD-Canada ↗
SpliceAI score
0.009 maximum delta

Recorded SpliceAI maximum delta score: 0.009. Refer to the recorded PP3/BP4 rationale for interpretation.

Applied · BP4, BP7 → SpliceAI ↗
ClinVar submissions
8 reported laboratory submissions

7 Likely benign · 1 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.

Applied · BS3 → OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
1 recorded samples

This variant has previously been reported in somatic cancers (COSMIC; COSV53744220, n = 1 times).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.

Context only
COSMIC ↗Cancer Hotspots ↗
For specialists

Technical detail

ACMG/AMP criteria under ClinGen ATM VCEP v1.6, with the data and sources behind each one.

28 criteria with recorded statuses: 3 met · 5 not met · 4 not assessed · 16 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.

Pathogenic
PVS1PS1PS2PS3PS4PM1PM2PM3PM4PM5PM6PP1PP2PP3PP4PP5
Benign
BA1BS1BS2BS3BS4BP1BP2BP3BP4BP5BP6BP7
Met Not met Not assessed Not applicable

For the three requested consequence/LoF criteria, the ATM VCEP rules yield PVS1 not applicable for this synonymous variant without predicted or observed splice disruption, PM4 not applicable because it is not stop-loss, and BP3 not applicable because the VCEP says not to use it.

Within the requested criterion group, only PS4 is applicable under the ATM VCEP, but it cannot be assessed because variant-specific case-control statistics are unavailable; PP4, PP5, BP5, and BP6 are explicitly not applicable.

PP3 is not met because SpliceAI maximum delta score 0.009 is below the VCEP pathogenic splicing threshold of 0.2.

BP4 is met at Supporting because SpliceAI maximum delta score 0.009 is at or below the VCEP benign splicing threshold of 0.1.

BP7 is met at Supporting because the variant is synonymous, a variant type explicitly included by the VCEP BP7 rule.

Met · 3

BS3 SupportingVCEPMet at Supporting: direct prime-editing classified c.6897C>T as Functional with High confidence and DeepATM_predicted=No. Details ▾Hide ▴
Reasoning

The exact row for NM_000051.4:c.6897C>T (F2299F; synonymous) in Sun et al. 2025 Supplementary Table S1 reports Classification=Functional, Confidence=High, and DeepATM_predicted=No. Per the VCEP-specific curation rule for this file, DeepATM_predicted=No with High confidence denotes a direct prime-editing measurement, and Classification=Functional assigns BS3_Supporting. This is consistent with the VCEP BS3 rule allowing Supporting when a variant rescues either an ATM-specific feature or radiosensitivity. The separately governing approved-assay methodology table was searched for c.6897C>T, p.Phe2299=, and p.F2299=, but contains no variant-specific result; therefore no additional assay strength is assigned from that table.

VCEP rule
Use when a variant rescues EITHER an ATM specifc feature OR rescues radiosensitivity.
Evidence considered
  • Sun et al. 2025 Supplementary Table S1, exact row c.6897C>T / F2299F / exon_47: Classification=Functional; Confidence=High; DeepATM_predicted=No; Combined_score=0.571099742195023.
  • The VCEP-specific rule for this table treats DeepATM_predicted=No with High, Medium-high, or Medium confidence as direct prime-editing measurement and assigns BS3_Supporting when Classification=Functional.
  • The VCEP CSPEC entry states: use BS3 Supporting when a variant rescues either an ATM-specific feature or radiosensitivity.
  • No c.6897C>T, p.Phe2299=, or p.F2299= entry was found in clingen_hbop_atm_supplementary_tables_1_and_2_v1.xlsx, so its assay-calibration text was not used to add strength.
Still missing
  • No c.6897C>T, p.Phe2299=, or p.F2299= entry was found in clingen_hbop_atm_supplementary_tables_1_and_2_v1.xlsx; that file is methodology calibration, not a per-variant results table.
Sources
vcep_suppl_tables1_pmid_40580951 ↗PMID:40580951 ↗vcep_clingen_hbop_atm_supplementary_tables_1_and_2_v1 ↗
BP4 SupportingVCEPMet: SpliceAI maximum delta score 0.009 is at or below the VCEP BP4 threshold of 0.1. Details ▾Hide ▴
Reasoning

The variant is synonymous, and the VCEP's splicing path is applicable. The VCEP defines BP4 splicing evidence as no predicted impact via SpliceAI ≤0.1. SpliceAI is available with a maximum delta score of 0.009, satisfying the VCEP cutoff. The searched Sun et al. Table S1 file contains the exact c.6897C>T row (F2299F; Classification Functional; Confidence High; DeepATM_predicted No); that functional result is not used to double-count or replace the SpliceAI evidence.

VCEP rule
* Splicing: No predicted impact via splicing (SpliceAI **≤0.1**).
Evidence considered
  • VCEP ATM v1.6 BP4 rule: splicing evidence requires no predicted impact via SpliceAI ≤0.1.
  • SpliceAI Lookup for NM_000051.4:c.6897C>T: DS_AG=0.000, DS_AL=0.009, DS_DG=0.001, DS_DL=0.007; maximum delta score=0.009.
  • Suppl_TableS1_PMID 40580951.xlsx exact row c.6897C>T / F2299F: Classification=Functional, Confidence=High, DeepATM_predicted=No; this functional result is not used for BP4.
Sources
cspec ↗spliceai ↗
BP7 SupportingVCEPMet: The variant is synonymous (p.Phe2299=), which is explicitly within the VCEP BP7 supporting scope. Details ▾Hide ▴
Reasoning

The variant is a synonymous substitution, NM_000051.4:c.6897C>T (p.Phe2299=), in exon 47. The VCEP BP7 supporting rule explicitly includes synonymous variants; therefore BP7 is applicable and met. BP7 is assigned from the variant type and VCEP scope, without reusing the SpliceAI prediction as an independent BP7 basis.

VCEP rule
* BP7: Use for synonymous and deep intronic variants defined as further than (but not including) +7 and further than (but not including) -21 at donor and acceptor sites, respectively.
Evidence considered
  • VCEP ATM v1.6 BP7 supporting rule: use for synonymous and deep intronic variants defined as further than (but not including) +7 and -21 at donor and acceptor sites, respectively.
  • Case variant facts: NM_000051.4:c.6897C>T, NP_000042.3:p.(Phe2299=), synonymous consequence, exon 47.
Sources
cspec ↗

Not met · 5 · evaluated, threshold not reached

PS3 VCEPNot met: direct prime-editing classified c.6897C>T as Functional with High confidence, not a variant failing to rescue an ATM-specific feature. Details ▾Hide ▴
Reasoning

The exact row for NM_000051.4:c.6897C>T (F2299F; synonymous) in Sun et al. 2025 Supplementary Table S1 reports Classification=Functional, Confidence=High, and DeepATM_predicted=No, indicating a direct prime-editing measurement with functional activity rather than a damaging result. Under the VCEP's governing PS3 rule, PS3 Supporting requires that a variant fail to rescue an ATM-specific feature; this result does not meet that condition. The separately governing approved-assay methodology table was searched for c.6897C>T, p.Phe2299=, and p.F2299=, but contains no variant-specific result, so its assay-calibration text cannot support PS3 for this variant.

VCEP rule
Use when a variant fails to rescue an ATM specifc feature, only (e.g. phosphorylation of ATM-specific targets). Do not use for radiosensitivity-only as that is not a feature specific to ATM deficiency
Evidence considered
  • Sun et al. 2025 Supplementary Table S1, exact row c.6897C>T / F2299F / exon_47: Classification=Functional; Confidence=High; DeepATM_predicted=No; Combined_score=0.571099742195023.
  • The VCEP-approved assay-calibration file was searched for c.6897C>T, p.Phe2299=, and p.F2299=; no exact variant entry was found. Its ATM kinase-activity table describes approved assays and calibrates PS3/BS3 Supporting, but does not report results for this variant.
  • No approved-assay result was identified that conflicts with the Functional direction in the Sun et al. row.
Still missing
  • No c.6897C>T, p.Phe2299=, or p.F2299= entry was found in clingen_hbop_atm_supplementary_tables_1_and_2_v1.xlsx; that file is methodology calibration, not a per-variant results table.
Sources
vcep_suppl_tables1_pmid_40580951 ↗PMID:40580951 ↗vcep_clingen_hbop_atm_supplementary_tables_1_and_2_v1 ↗
PM2 VCEPNot met: the highest gnomAD subpopulation AF is 0.00271185% in v4.1, exceeding the VCEP's ≤0.001% PM2 threshold. Details ▾Hide ▴
Reasoning

The ATM VCEP applies PM2 at Supporting strength when frequency is at most 0.001% in the gnomAD subpopulation with the highest frequency, with a single-observation exception only when n=1 in one subpopulation and absent from all others. The highest observed subpopulation frequency is 0.00352051% (4/113620 alleles; European non-Finnish) in gnomAD v2.1 and 0.00271185% (32/1180008 alleles; European non-Finnish) in gnomAD v4.1, so the threshold is exceeded and the n=1 exception does not apply.

VCEP rule
Frequency **≤.001%** in gnomAD subpopulation with the highest frequency ... Exception: If >0.001% but n=1 in a single subpopulation (not present in any other subpopulation), that is sufficiently rare and PM2\_supporting would apply.
Evidence considered
  • ATM VCEP v1.6 PM2 rule: Frequency ≤.001% in the gnomAD subpopulation with the highest frequency; the n=1 single-subpopulation exception does not apply here.
  • gnomAD v2.1 highest subpopulation: European (non-Finnish), AF = 3.520506953001232e-05 (0.00352051%), 4/113620 alleles, homozygotes = 0.
  • gnomAD v4.1 highest subpopulation: European (non-Finnish), AF = 2.7118460213829058e-05 (0.00271185%), 32/1180008 alleles, homozygotes = 0.
Sources
cspec ↗gnomad_v2 ↗gnomad_v4 ↗
PP3 VCEPNot met: SpliceAI maximum delta score 0.009 is below the VCEP PP3 threshold of 0.2. Details ▾Hide ▴
Reasoning

The variant is synonymous (NM_000051.4:c.6897C>T; p.Phe2299=), so the VCEP's splicing path applies. The VCEP requires predicted splice impact via SpliceAI ≥0.2 for silent variants. SpliceAI is available and the maximum delta score is 0.009 (DS_AG 0.000, DS_AL 0.009, DS_DG 0.001, DS_DL 0.007), which does not meet PP3. The searched Sun et al. Table S1 file contains the exact c.6897C>T row (F2299F; Classification Functional; Confidence High; DeepATM_predicted No), but that row does not pre-assign PP3 and its functional classification is not used as computational evidence.

VCEP rule
* Splicing: Predicted impact via splicing (SpliceAI **≥0.2**) for silent, missense/in-frame and for intronic variants outside of donor and acceptor 1,2 sites.
Evidence considered
  • VCEP ATM v1.6 PP3 rule: splicing evidence for silent variants requires predicted impact via SpliceAI ≥0.2.
  • SpliceAI Lookup for NM_000051.4:c.6897C>T: DS_AG=0.000, DS_AL=0.009, DS_DG=0.001, DS_DL=0.007; maximum delta score=0.009.
  • Suppl_TableS1_PMID 40580951.xlsx exact row c.6897C>T / F2299F: Classification=Functional, Confidence=High, DeepATM_predicted=No; this is not used to assign PP3.
Sources
cspec ↗spliceai ↗
BA1 VCEPNot met: gnomAD grpmax filtering AF is 0.001962% in v4.1, below the VCEP's >0.5% BA1 threshold. Details ▾Hide ▴
Reasoning

The ATM VCEP applies BA1 when the gnomAD group-maximum filtering allele frequency exceeds 0.5%. This variant's grpmax filtering AF is 0.00001122 (0.001122%) in gnomAD v2.1 and 0.00001962 (0.001962%) in gnomAD v4.1, both far below 0.5%; therefore BA1 is not met.

VCEP rule
Grpmax Filtering AF **>.5%** in gnomAD
Evidence considered
  • ATM VCEP v1.6 BA1 rule: Grpmax Filtering AF >.5% in gnomAD.
  • gnomAD v2.1: grpmax FAF = 1.122e-05 (0.001122%).
  • gnomAD v4.1: joint grpmax FAF = 1.962e-05 (0.001962%).
Sources
cspec ↗gnomad_v2 ↗gnomad_v4 ↗
BS1 VCEPNot met: gnomAD grpmax filtering AF is 0.001962% in v4.1, below the VCEP's >0.05% BS1 threshold. Details ▾Hide ▴
Reasoning

The ATM VCEP applies BS1 when the gnomAD group-maximum filtering allele frequency exceeds 0.05%. This variant's grpmax filtering AF is 0.00001122 (0.001122%) in gnomAD v2.1 and 0.00001962 (0.001962%) in gnomAD v4.1, both below 0.05%; therefore BS1 is not met.

VCEP rule
Grpmax Filtering AF **>.05%** in gnomAD
Evidence considered
  • ATM VCEP v1.6 BS1 rule: Grpmax Filtering AF >.05% in gnomAD.
  • gnomAD v2.1: grpmax FAF = 1.122e-05 (0.001122%).
  • gnomAD v4.1: joint grpmax FAF = 1.962e-05 (0.001962%).
Sources
cspec ↗gnomad_v2 ↗gnomad_v4 ↗

Not assessed · 4 · no assessment recorded

PS4 VCEPNot assessed: no variant-specific case-control p-value, odds ratio, relative risk, hazard ratio, or lower 95% confidence interval is available for the PS4 thresholds. Details ▾Hide ▴
Reasoning

The ATM VCEP permits PS4_Strong only for a case-control study with p-value <=.05 and either an odds ratio, hazard ratio, or relative risk >=2 or a lower 95% confidence interval >=1.5. The available evidence contains no variant-specific case-control p-value, effect estimate, or confidence interval for NM_000051.4:c.6897C>T, so the rule cannot be evaluated.

VCEP rule
Case-control studies; p-value ≤.05 **and** (Odds ratio, hazard ratio, or relative risk ≥2 **or** lower 95% CI ≥1.5).
Evidence considered
  • No variant-specific case-control enrichment dataset was identified for NM_000051.4:c.6897C>T (NP_000042.3:p.(Phe2299=)); therefore no p-value, effect estimate, or confidence interval can be substituted into the PS4 rule.
Still missing
  • Variant-specific case-control study results including p-value and odds ratio, hazard ratio, or relative risk with its lower 95% confidence interval are unavailable.
Sources
cspec ↗PMID:18163131 ↗PMID:24418350 ↗
PM3 VCEPNot assessed: no governing-table entry or affected A-T proband phase evidence is available to assign PM3 points. Details ▾Hide ▴
Reasoning

The ATM VCEP PM3 rule requires the variant to be detected in trans with a pathogenic variant in a recessive disorder and assigns points by affected A-T proband phenotype and phase. The governing ATM_PM3_BP2_1.6.pdf table was searched for c.6897C>T, p.Phe2299=, and p.F2299=; no entry was found. The available case evidence contains no affected A-T proband observation, co-occurring pathogenic ATM variant, phase result, or phenotype classification from which PM3 points could be assigned.

VCEP rule
For recessive disorders, detected in trans with a pathogenic variant
Evidence considered
  • ATM_PM3_BP2_1.6.pdf, PM3 section and Ataxia Telangiectasia PM3|BP2 table: searches for c.6897C>T, p.Phe2299=, and p.F2299= returned no matching variant row.
  • Case evidence for NM_000051.4:c.6897C>T provides no affected A-T proband, co-occurring pathogenic ATM variant, phase, or PM3 phenotype classification.
  • ATM PM3/BP2 table: PM3 points per unrelated A-T proband are 4.0 or 2.0 for confirmed in-trans observations depending on phenotype, with lower values for unknown phase, unidentified/VUS second variant, or homozygosity; no applicable observation is available here.
Still missing
  • ATM_PM3_BP2_1.6.pdf was searched for c.6897C>T, p.Phe2299=, and p.F2299=; no entry for this variant was found.
  • No affected A-T proband observation with a pathogenic or likely pathogenic variant in trans and an applicable phenotype classification is available.
  • No parental or other phase evidence is available to establish trans, phase unknown, cis, or homozygous status.
Sources
cspec ↗vcep_atm_pm3_bp2_1_6 ↗
PP1 VCEPNot assessed: no affected relatives, parental testing, phase information, or segregation count is documented to meet the VCEP's AR PP1 requirements. Details ▾Hide ▴
Reasoning

The VCEP permits PP1 only for the AR condition, requires affected relatives to have both variants identified in the proband, and assigns Supporting, Moderate, or Strong according to segregation in 1, 2, or at least 3 affected relatives. The available case evidence contains no documented affected relatives, parental testing, phase information, meioses, or segregation analysis, and does not establish an AR ataxia-telangiectasia phenotype; PP1 cannot be assessed.

VCEP rule
AR Condition: Affected relatives must have both variants identified in proband. ... AD Condition – Do not use: Co-segregation analysis in lower-penetrance genes can lead to false positive results (PMID 32773770) ... AR Condition: Segregation in ≥3 affected relatives ... AR Condition: Segregation in 2 affected relatives ... AR Condition: Segregation in 1 affected relative
Evidence considered
  • ATM VCEP v1.6 CSPEC PP1 entry requires both variants in the proband for the AR condition and states that the AD condition should not use co-segregation analysis.
  • ATM VCEP v1.6 CSPEC PP1 strength rows specify Supporting for segregation in 1 affected relative, Moderate for 2 affected relatives, and Strong for at least 3 affected relatives.
  • No case-specific affected-relative, parental, phase, meiosis, or segregation result is documented in the reviewed case evidence.
Still missing
  • Documented inheritance context and phenotype
  • Affected-relative testing and segregation count
  • Parental testing and phase information
Sources
cspec ↗
BP2 VCEPNot assessed: no governing-table entry or qualifying unaffected adult cis/trans observation is available to assign BP2 points. Details ▾Hide ▴
Reasoning

The ATM VCEP BP2 rule requires observation in trans with a pathogenic variant for a fully penetrant dominant disorder or in cis with a pathogenic variant in any inheritance pattern; its ATM PM3/BP2 table assigns BP2 points for unaffected adult non-A-T probands. The governing ATM_PM3_BP2_1.6.pdf table was searched for c.6897C>T, p.Phe2299=, and p.F2299=; no entry was found. The available case evidence contains no qualifying unaffected adult proband observation, co-occurring pathogenic variant, or cis/trans phase information, so no BP2 points or strength can be assigned.

VCEP rule
Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.
Evidence considered
  • ATM_PM3_BP2_1.6.pdf, BP2 section and Ataxia Telangiectasia PM3|BP2 table: searches for c.6897C>T, p.Phe2299=, and p.F2299= returned no matching variant row.
  • Case evidence for NM_000051.4:c.6897C>T provides no qualifying unaffected adult non-A-T proband, co-occurring pathogenic ATM variant, or cis/trans phase observation.
  • ATM PM3/BP2 table: BP2 points per unaffected non-A-T adult proband are -4.0 for confirmed trans, -2.0 for phase unknown, and -2.0 or -1.0 for homozygous laboratory or database settings; no applicable observation is available here.
Still missing
  • ATM_PM3_BP2_1.6.pdf was searched for c.6897C>T, p.Phe2299=, and p.F2299=; no entry for this variant was found.
  • No unaffected adult non-A-T proband observation with a co-occurring pathogenic or likely pathogenic ATM variant is available.
  • No phase evidence is available to establish cis or trans, and no laboratory-setting or database-setting classification applies without a qualifying observation.
Sources
cspec ↗vcep_atm_pm3_bp2_1_6 ↗
Not applicable · 16· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/ANot applicable: the variant is synonymous and SpliceAI maximum delta score is 0.009, with no predicted or observed splice defect supporting ATM PVS1. Details ▾Hide ▴
Reasoning

NM_000051.4:c.6897C>T is a synonymous exon 47 variant, NP_000042.3:p.(Phe2299=), not one of the VCEP's listed null variant classes. The VCEP also permits PVS1 for a predicted splice defect, but SpliceAI shows no significant splice impact (maximum delta score 0.009), and no observed RNA splice defect is available. Therefore the ATM PVS1 decision tree does not apply to this variant. The governing ATM_PVS1_1.6.pdf file was searched for c.6897C>T, p.Phe2299=, and p.F2299=; no variant-specific entry was found.

VCEP rule
Null variant (nonsense, frameshift, canonical +/-1 or 2 splice sites, initiation codon, single or multi-exon deletion) in a gene where loss of function (LOF) is a known mechanism of disease ... PVS1: Predicted splice defect
Evidence considered
  • Variant consequence: NM_000051.4:c.6897C>T is synonymous in exon 47 and encodes NP_000042.3:p.(Phe2299=).
  • The ATM PVS1 guide defines eligible null variants as nonsense, frameshift, canonical +/-1 or 2 splice-site, initiation-codon, or single/multi-exon deletion variants; this variant is none of those.
  • The VCEP CSPEC entry states PVS1 applies to a predicted splice defect; SpliceAI maximum delta score is 0.009, indicating no significant predicted splice impact.
  • The governing ATM_PVS1_1.6.pdf text was searched for c.6897C>T, p.Phe2299=, and p.F2299= with no matching variant-specific entry.
Still missing
  • No entry for c.6897C>T, p.Phe2299=, or p.F2299= was found in ATM_PVS1_1.6.pdf.txt.
  • No observed RNA splice assay result is available.
Sources
cspec ↗vcep_atm_pvs1_1_6 ↗spliceai ↗
PS1 N/ANot applicable: c.6897C>T is synonymous (p.Phe2299=), and ATM_PS1_1.6.pdf contains no matching variant entry. Details ▾Hide ▴
Reasoning

The variant is synonymous (c.6897C>T; p.Phe2299= / p.F2299=), not a missense or splice variant eligible for the ATM PS1 rule. The governing ATM_PS1_1.6.pdf was searched for c.6897C>T, p.Phe2299=, and p.F2299=; no entry for this variant was found.

VCEP rule
* Use for missense changes as long as splicing is ruled-out for both alterations either by RNA analysis and/or in silico splice predictions
Evidence considered
  • Case normalization identifies NM_000051.4:c.6897C>T as synonymous, NP_000042.3:p.(Phe2299=) / p.(F2299=).
  • ATM_PS1_1.6.pdf was searched for c.6897C>T, p.Phe2299=, and p.F2299=; no matching row was found.
Still missing
  • ATM_PS1_1.6.pdf was searched for c.6897C>T, p.Phe2299=, and p.F2299=; no entry was found.
Sources
cspec ↗vcep_atm_ps1_1_6 ↗
PS2 VCEPNot applicable: the ATM VCEP states that informative de novo occurrences have not been observed for either autosomal-dominant or autosomal-recessive disease. Details ▾Hide ▴
Reasoning

The ATM VCEP marks PS2 not applicable and instructs that informative de novo occurrences have not been observed for AD or AR disease; therefore confirmed de novo status cannot be used for this ATM interpretation.

VCEP rule
Do not use for AD or AR disease: Informative de novo occurrences have not yet been observed and de novo AR conditions are unlikely to be informed by phase
Evidence considered
  • ATM VCEP v1.6 CSPEC PS2 entry: applicability is Not applicable; instruction states, "Do not use for AD or AR disease: Informative de novo occurrences have not yet been observed and de novo AR conditions are unlikely to be informed by phase".
Sources
cspec ↗
PM1 VCEPNot applicable: ATM Version 1.6 marks PM1 as Not Applicable, and no authoritative ATM domain-table entry is present. Details ▾Hide ▴
Reasoning

The ATM Version 1.6 CSPEC marks PM1 as Not Applicable. The vcep_materials.json domain_tables object has no ATM entry, so no authoritative approved critical-domain list is available to support PM1; the variant is also synonymous at residue 2299.

VCEP rule
Not Applicable
Evidence considered
  • The ATM Version 1.6 CSPEC entry for PM1 states applicability: Not Applicable.
  • vcep_materials.json has an empty domain_tables object for ATM; residue 2299 therefore cannot be assigned to an approved PM1 domain from that source.
Sources
cspec ↗
PM4 N/ANot applicable: p.(Phe2299=) is synonymous and does not represent the VCEP-defined PM4 stop-loss variant type. Details ▾Hide ▴
Reasoning

The ATM VCEP specifies PM4 for stop-loss variants. NM_000051.4:c.6897C>T is synonymous, producing p.(Phe2299=), and is neither a stop-loss nor a protein length-changing variant. PM4 is therefore not applicable.

VCEP rule
Use for stop-loss variants.
Evidence considered
  • The ATM VCEP PM4 rule states: Use for stop-loss variants.
  • The case variant is synonymous, NM_000051.4:c.6897C>T, encoding NP_000042.3:p.(Phe2299=), with no protein length change.
Sources
cspec ↗
PM5 N/ANot applicable: PM5 requires an NMD-prone truncating or qualifying splice variant upstream of p.Leu3048, whereas this variant is synonymous. Details ▾Hide ▴
Reasoning

The ATM Version 1.6 PM5 rule applies to NMD-prone truncating DNA or splice variants with premature termination codons upstream of p.Leu3048, under the stated PVS1 requirements. This variant is synonymous, not truncating or splice, so PM5 does not apply.

VCEP rule
* DNA Variants: Apply to all NMD-prone, truncating variants receiving PVS1 (must be at VeryStrong) with premature termination codons upstream of p.Leu3048 * Splice Variants: Apply only to observed (not predicted) NMD-prone, truncating variants receiving PVS1(RNA) (must be at VeryStrong with high-quality RNA data) with premature termination codons upstream of p.Leu3048. This is not applicable for predicted splice impact without RNA data or PVS1(RNA) at reduced strength.
Evidence considered
  • The ATM Version 1.6 PM5 rule specifies NMD-prone truncating DNA variants or observed NMD-prone truncating splice variants with premature termination codons upstream of p.Leu3048.
  • Case evidence identifies c.6897C>T as synonymous, p.Phe2299= / p.F2299=, not a truncating or splice variant.
Sources
cspec ↗
PM6 VCEPNot applicable: the ATM VCEP states that informative de novo occurrences have not been observed for either autosomal-dominant or autosomal-recessive disease. Details ▾Hide ▴
Reasoning

The ATM VCEP marks PM6 not applicable and instructs that informative de novo occurrences have not been observed for AD or AR disease; an assumed de novo finding therefore cannot receive PM6.

VCEP rule
Do not use for AD or AR disease: Informative de novo occurrences have not yet been observed and de novo AR conditions are unlikely to be informed by phase
Evidence considered
  • ATM VCEP v1.6 CSPEC PM6 entry: applicability is Not applicable; instruction states, "Do not use for AD or AR disease: Informative de novo occurrences have not yet been observed and de novo AR conditions are unlikely to be informed by phase".
Sources
cspec ↗
PP2 VCEPNot applicable: the ATM Version 1.6 CSPEC explicitly marks PP2 as Not Applicable. Details ▾Hide ▴
Reasoning

The ATM Version 1.6 CSPEC marks PP2 as Not Applicable; therefore no gene-level missense-mechanism evidence can be assigned under this VCEP criterion.

VCEP rule
Not Applicable
Evidence considered
  • The ATM Version 1.6 CSPEC entry for PP2 states applicability: Not Applicable.
Sources
cspec ↗
PP4 VCEPNot applicable: the VCEP excludes PP4 for hereditary breast cancer and incorporates ataxia-telangiectasia phenotype evidence into PM3/BP2. Details ▾Hide ▴
Reasoning

The ATM VCEP marks PP4 not applicable for both relevant disease contexts: it excludes PP4 for autosomal-dominant breast cancer because of genetic heterogeneity and excludes it as a separate line for autosomal-recessive ataxia telangiectasia because the phenotype evidence is incorporated into the PM3/BP2 table.

VCEP rule
Autosomal Dominant: do not use as breast cancer is a disease with multiple genetic etiology (genetic heterogeneity) and there are no features that can readily distinguish hereditary from sporadic causes. ... Autosomal Recessive: do not use as a separate line of evidence. Such evidence is built into the Ataxia Telangiectasia PM3|BP2 table
Evidence considered
  • The VCEP criterion entry states: Autosomal Dominant: do not use as breast cancer is a disease with multiple genetic etiology (genetic heterogeneity) and there are no features that can readily distinguish hereditary from sporadic causes.
  • The VCEP criterion entry states: Autosomal Recessive: do not use as a separate line of evidence. Such evidence is built into the Ataxia Telangiectasia PM3|BP2 table.
Sources
cspec ↗
PP5 VCEPNot applicable: the ATM VCEP explicitly prohibits PP5, regardless of the available ClinVar classifications or literature references. Details ▾Hide ▴
Reasoning

The ATM VCEP marks PP5 not applicable and states that this criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. The available ClinVar submissions therefore cannot support PP5 under this VCEP.

VCEP rule
This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.
Evidence considered
  • The VCEP marks PP5 as Not Applicable for this VCEP; ClinVar reports Likely benign or Benign submissions, not an independently usable PP5 evidence basis.
Sources
cspec ↗
BS2 VCEPNot applicable: the ATM VCEP excludes BS2 because ATM has incomplete penetrance, regardless of zero observed homozygotes. Details ▾Hide ▴
Reasoning

The ATM VCEP marks BS2 not applicable and states not to use it because ATM has incomplete penetrance. The absence of homozygotes in gnomAD does not change that governing applicability decision.

VCEP rule
Do not use: ATM has incomplete penetrance.
Evidence considered
  • ATM VCEP v1.6 BS2 applicability: Do not use: ATM has incomplete penetrance.
  • gnomAD v2.1 and v4.1 each report zero homozygotes, but this evidence cannot activate a VCEP-excluded criterion.
Sources
cspec ↗
BS4 VCEPNot applicable: the ATM VCEP excludes BS4 because informative lack-of-segregation instances in A-T families are too rare for weight. Details ▾Hide ▴
Reasoning

The ATM VCEP marks BS4 not applicable. Its instructions state that lack-of-segregation evidence is not weighted for ATM autosomal-recessive ataxia-telangiectasia families because informative instances are too rare, and caution against false positives in low-penetrance autosomal-dominant analysis.

VCEP rule
AD Condition: Co-segregation analysis in low penetrance genes can lead to false positive results (PMID 32773770) ... AR Condition: Informative instances of lack of co-segregation in A-T families are too rare to be considered for weight at this time and can also be considered for BP2 if biallelic unaffected patients are observed in an A-T family.
Evidence considered
  • ATM VCEP v1.6 CSPEC BS4 entry: applicability is Not applicable; its instructions address low-penetrance AD false positives and state that informative lack-of-segregation instances in A-T families are too rare to receive weight.
Sources
cspec ↗
BP1 VCEPNot applicable: the ATM Version 1.6 CSPEC explicitly marks BP1 as Not Applicable. Details ▾Hide ▴
Reasoning

The ATM Version 1.6 CSPEC marks BP1 as Not Applicable; no BP1 evidence may be assigned under this VCEP criterion.

VCEP rule
Not Applicable
Evidence considered
  • The ATM Version 1.6 CSPEC entry for BP1 states applicability: Not Applicable.
Sources
cspec ↗
BP3 VCEPNot applicable: the ATM VCEP explicitly marks BP3 as not applicable and instructs curators not to use it. Details ▾Hide ▴
Reasoning

The ATM VCEP CSPEC entry marks BP3 as not applicable and instructs curators not to use it. This synonymous exon 47 variant therefore cannot receive BP3 under the governing ATM VCEP framework, regardless of its repeat-region or protein-length context.

VCEP rule
Do not use.
Evidence considered
  • The ATM VCEP CSPEC entry lists BP3 applicability as Not applicable and its instruction as Do not use.
  • The variant is synonymous in exon 47 and does not create a protein length change.
Sources
cspec ↗
BP5 VCEPNot applicable: the ATM VCEP explicitly says not to use BP5 because multiple pathogenic variants may coexist without a noticeable phenotype difference. Details ▾Hide ▴
Reasoning

The ATM VCEP marks BP5 not applicable and instructs reviewers not to use it because cases with multiple pathogenic variants have been observed without a noticeable phenotype difference; ATM's low penetrance also increases the likelihood of other pathogenic variants occurring together.

VCEP rule
Do not use: Cases with multiple pathogenic variants have been observed with no noticeable difference in phenotype (e.g. BRCA1 and BRCA2). In addition, ATM has low penetrance and will naturally occur with other pathogenic variants more frequently due to higher tolerance/presence in the general population.
Evidence considered
  • The VCEP instruction for BP5 is: Do not use: Cases with multiple pathogenic variants have been observed with no noticeable difference in phenotype (e.g. BRCA1 and BRCA2). In addition, ATM has low penetrance and will naturally occur with other pathogenic variants more frequently due to higher tolerance/presence in the general population.
Sources
cspec ↗
BP6 VCEPNot applicable: the ATM VCEP explicitly prohibits BP6, regardless of the available ClinVar benign or likely benign submissions. Details ▾Hide ▴
Reasoning

The ATM VCEP marks BP6 not applicable and states that this criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. The available ClinVar benign or likely benign submissions therefore cannot support BP6 under this VCEP.

VCEP rule
This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.
Evidence considered
  • The VCEP marks BP6 as Not Applicable for this VCEP; ClinVar reports Likely benign or Benign submissions, but BP6 is prohibited by the governing VCEP.
Sources
cspec ↗

Identifiers

Gene
ATM
Transcript
NM_000051.4
Coding (HGVS c.)
NM_000051.4:c.6897C>T
Protein (HGVS p.)
NP_000042.3:p.(Phe2299=)
GRCh38
chr11:108326147 C>T
GRCh37
chr11:108196874 C>T
Location and type
Exon 47 · synonymous
ClinVar
230580
COSMIC
COSV53744220

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 33 / 1,613,946 alleles AF 2.04e-05 · 0 homozygotes · FAF 1.96e-05
gnomAD v2.1 4 / 251,296 alleles AF 1.59e-05 · 0 homozygotes · FAF 1.12e-05
gnomAD-Canada v1.0 Allele count data not recorded

By genetic ancestry

gnomAD v4.1

AF 2e-05 · 33 / 1,613,946 alleles · 0 hom · FAF 2e-05
European (non-Finnish)32 / 1,180,008 2.7e-05
Remaining individuals1 / 62,480 1.6e-05
0 alternate alleles recorded in 8 other groups: Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American.

gnomAD v2.1

AF 1.6e-05 · 4 / 251,296 alleles · 0 hom · FAF 1.1e-05
European (non-Finnish)4 / 113,620 3.5e-05
0 alternate alleles recorded in 7 other groups: African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian.

Statements

gnomAD v4.1

This variant is present in gnomAD v4.1 (AF= 2.04468e-05; MAF= 0.00204%, 33/1613946 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.71185e-05; MAF= 0.00271%, 32/1180008 alleles, homozygotes = 0); grpmax FAF= 1.962e-05.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 1.59175e-05; MAF= 0.00159%, 4/251296 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.52051e-05; MAF= 0.00352%, 4/113620 alleles, homozygotes = 0); grpmax FAF= 1.122e-05.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

SpliceAI and Pangolin

SpliceAI acceptor lossat -89 bp
0.009
SpliceAI acceptor gainat +13 bp
0.000
SpliceAI donor lossat +78 bp
0.007
SpliceAI donor gainat -6 bp
0.001
Pangolin splice lossmagnitude shown
-0.047
Pangolin splice gain
0.001

Other predictors

REVEL
Not available
BayesDel
Not available

How the predictions were used

BP4 SupportingVCEPMet: SpliceAI maximum delta score 0.009 is at or below the VCEP BP4 threshold of 0.1. Details ▾Hide ▴
Reasoning

The variant is synonymous, and the VCEP's splicing path is applicable. The VCEP defines BP4 splicing evidence as no predicted impact via SpliceAI ≤0.1. SpliceAI is available with a maximum delta score of 0.009, satisfying the VCEP cutoff. The searched Sun et al. Table S1 file contains the exact c.6897C>T row (F2299F; Classification Functional; Confidence High; DeepATM_predicted No); that functional result is not used to double-count or replace the SpliceAI evidence.

VCEP rule
* Splicing: No predicted impact via splicing (SpliceAI **≤0.1**).
Evidence considered
  • VCEP ATM v1.6 BP4 rule: splicing evidence requires no predicted impact via SpliceAI ≤0.1.
  • SpliceAI Lookup for NM_000051.4:c.6897C>T: DS_AG=0.000, DS_AL=0.009, DS_DG=0.001, DS_DL=0.007; maximum delta score=0.009.
  • Suppl_TableS1_PMID 40580951.xlsx exact row c.6897C>T / F2299F: Classification=Functional, Confidence=High, DeepATM_predicted=No; this functional result is not used for BP4.
Sources
cspec ↗spliceai ↗
BP7 SupportingVCEPMet: The variant is synonymous (p.Phe2299=), which is explicitly within the VCEP BP7 supporting scope. Details ▾Hide ▴
Reasoning

The variant is a synonymous substitution, NM_000051.4:c.6897C>T (p.Phe2299=), in exon 47. The VCEP BP7 supporting rule explicitly includes synonymous variants; therefore BP7 is applicable and met. BP7 is assigned from the variant type and VCEP scope, without reusing the SpliceAI prediction as an independent BP7 basis.

VCEP rule
* BP7: Use for synonymous and deep intronic variants defined as further than (but not including) +7 and further than (but not including) -21 at donor and acceptor sites, respectively.
Evidence considered
  • VCEP ATM v1.6 BP7 supporting rule: use for synonymous and deep intronic variants defined as further than (but not including) +7 and -21 at donor and acceptor sites, respectively.
  • Case variant facts: NM_000051.4:c.6897C>T, NP_000042.3:p.(Phe2299=), synonymous consequence, exon 47.
Sources
cspec ↗
PP3 VCEPNot met: SpliceAI maximum delta score 0.009 is below the VCEP PP3 threshold of 0.2. Details ▾Hide ▴
Reasoning

The variant is synonymous (NM_000051.4:c.6897C>T; p.Phe2299=), so the VCEP's splicing path applies. The VCEP requires predicted splice impact via SpliceAI ≥0.2 for silent variants. SpliceAI is available and the maximum delta score is 0.009 (DS_AG 0.000, DS_AL 0.009, DS_DG 0.001, DS_DL 0.007), which does not meet PP3. The searched Sun et al. Table S1 file contains the exact c.6897C>T row (F2299F; Classification Functional; Confidence High; DeepATM_predicted No), but that row does not pre-assign PP3 and its functional classification is not used as computational evidence.

VCEP rule
* Splicing: Predicted impact via splicing (SpliceAI **≥0.2**) for silent, missense/in-frame and for intronic variants outside of donor and acceptor 1,2 sites.
Evidence considered
  • VCEP ATM v1.6 PP3 rule: splicing evidence for silent variants requires predicted impact via SpliceAI ≥0.2.
  • SpliceAI Lookup for NM_000051.4:c.6897C>T: DS_AG=0.000, DS_AL=0.009, DS_DG=0.001, DS_DL=0.007; maximum delta score=0.009.
  • Suppl_TableS1_PMID 40580951.xlsx exact row c.6897C>T / F2299F: Classification=Functional, Confidence=High, DeepATM_predicted=No; this is not used to assign PP3.
Sources
cspec ↗spliceai ↗

Statement

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01).

7 paper records listed. 1 cited in the classification. None of the listed paper records explicitly indicates that the variant is named.

Cited in the classification

  • Sun et al. 2025
    Sun et al. 2025 Supplementary Table S1 contains the exact ATM synonymous variant c.6897C>T (F2299F) row. The row reports Combined_score 0.571099742195023, Classification Functional, Confidence High, and DeepATM_predicted No; under the VCEP file-specific rule this is a direct prime-editing measurement supporting BS3 at Supporting strength and not PS3.
    → BS3 · supporting Names this variant
    PMID 40580951 ↗
    Source detail
    108326147 C T c.6897C>T F2299F exon_47 11 Synonymous 2299 NA NA NA NA NA 2.044678074731e-05 Likely benign 0.571099742195023 Functional High No

    Location Table S1 converted full text, row 22059

    Context Sun et al. 2025 functional assessment of ATM SNVs using prime editing and deep learning; the exact row is marked DeepATM_predicted=No and Confidence=High, which the VCEP table policy treats as direct prime-editing measurement.

Other 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.
    No paper-specific finding is recorded.
    PMID 25741868 ↗
  • The emerging landscape of breast cancer susceptibility.
    Stratton MR et al. · 2008
    This review does not explicitly mention ATM c.6897C>T or NP_000042.3:p.(F2299=). It describes ATM as a rare moderate-penetrance breast cancer susceptibility gene and summarizes approximately two- to fourfold relative risk for ATM mutations, but it provides no variant-specific case-control data for this synonymous variant.
    Does not name this variant
    PMID 18163131 ↗
    Quoted passage
    In CHEK2, ATM, BRIP1 and PALB2, most of the disease-causing mutations result in premature protein truncation or nonsense-mediated RNA decay through nonsense codons or translational frameshifts. A small proportion is likely to be rare missense variants that disrupt critical functions.

    Rare moderate-penetrance breast cancer susceptibility genes, page 18

  • Ataxia-Telangiectasia.
    No paper-specific finding is recorded.
    PMID 20301790 ↗
  • EFNS/ENS Consensus on the diagnosis and management of chronic ataxias in adulthood.
    This consensus paper does not mention the exact ATM variant c.6897C>T or NP_000042.3:p.(F2299=). It discusses ataxia telangiectasia as a recessive ataxia and diagnostic considerations, but provides no variant-specific phenotype or case-control evidence for this variant.
    Does not name this variant
    PMID 24418350 ↗
    Quoted passage
    The second most frequent recessive ataxia globally is ataxia telangiectasia, with the exception of North Africa where this is ataxia with vitamin E deficiency [15,16].

    Recessive family history, paragraph 4

  • ATM-Related Cancer Predisposition.
    No paper-specific finding is recorded.
    PMID 42258614 ↗
  • EFNS guidelines on the molecular diagnosis of ataxias and spastic paraplegias.
    No paper-specific finding is recorded.
    PMID 20050888 ↗
  • Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
    No paper-specific finding is recorded.
    PMID 28492532 ↗

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

gnomAD v4.1 33 / 1,613,946 recorded alleles Open source ↗
gnomAD v2.1 Captured gnomAD v2.1 source record Open source ↗
SpliceAI Lookup Recorded maximum delta 0.009 Open source ↗
ClinVar 7 Likely benign · 1 Benign Open source ↗
COSMIC Captured COSMIC source record Open source ↗
Cancer hotspots Captured Cancer Hotspots source record Open source ↗
OncoKB Captured OncoKB source record Open source ↗
ClinGen CSpec Captured ClinGen CSpec source record Open source ↗

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= 2.04468e-05; MAF= 0.00204%, 33/1613946 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.71185e-05; MAF= 0.00271%, 32/1180008 alleles, homozygotes = 0); grpmax FAF= 1.962e-05.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 1.59175e-05; MAF= 0.00159%, 4/251296 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.52051e-05; MAF= 0.00352%, 4/113620 alleles, homozygotes = 0); grpmax FAF= 1.122e-05.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

ClinVar

This variant has been reported in ClinVar as Likely benign (7 clinical laboratories) and as Benign (1 clinical laboratory). (ClinVarID = 230580)

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01).

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 previously been reported in somatic cancers (COSMIC; COSV53744220, n = 1 times).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.