ATMc.2377-18T>CUncertain significance

Print report

Variant interpretation report

ATM c.2377-18T>C, p.?

NM_000051.4:c.2377-18T>C NP_000042.3:p.? Unknown · intron 15 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

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: 1

Pathogenic criteria applied · 0

No pathogenic criterion marked as applied in the recorded assessment.

Benign criteria applied · 1

BP4Supporting

BP4 · supporting

Met at supporting: SpliceAI maximum delta 0.059 meets the ATM VCEP BP4 splicing threshold of <=0.1.

Recorded classification: Uncertain significance

VUS: BP4 (supporting) indicates no predicted splice impact, but no pathogenic or benign combination rule is satisfied under the ATM VCEP framework.

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

15 / 1,597,506 alleles

gnomAD v4.1: 15 / 1,597,506 alleles. Recorded AF 9.38964e-06. Recorded homozygote count 0.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 1.9931e-05; MAF= 0.00199%, 5/250866 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.52454e-05; MAF= 0.00352%, 4/113490 alleles, homozygotes = 0); grpmax FAF= 1.123e-05.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

No listed criterion applied

gnomAD v4.1 ↗gnomAD v2.1 ↗gnomAD-Canada ↗

SpliceAI score

0.059 maximum delta

Recorded SpliceAI maximum delta score: 0.059. Refer to the recorded PP3/BP4 rationale for interpretation.

Applied · BP4 → SpliceAI ↗

ClinVar submissions

5 reported laboratory submissions

5 Likely benign. ClinVar API review status: criteria provided, multiple submitters, no conflicts.

Context only ClinVar ↗

No screenshot for this evidence

Functional evidence

Not recorded

No standalone functional evidence summary is recorded in evidence_summary.functional.

No listed criterion applied OncoKB ↗

Somatic evidence

No matching record reported

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

Context only COSMIC ↗

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: 1 met · 5 not met · 7 not assessed · 15 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.

Pathogenic

PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5

Benign

BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7

Met Not met Not assessed Not applicable

The governing ATM VCEP version 1.6 specification excludes PS2, PM6, and BS4; PP1 is potentially applicable only for autosomal-recessive segregation but cannot be assessed without documented affected-relative and phase data.

Within this group, PS4 is not assessed because qualifying case-control enrichment data are absent; PP4, PP5, BP5, and BP6 are not applicable under the ATM VCEP v1.6 specification.

The ClinVar record is exact-variant but has zero expert-panel submissions, so its five clinical-laboratory Likely benign submissions cannot activate PP5 or BP6.

The governing ATM VCEP v1.6 was applied before generic ACMG defaults.

BA1 and BS1 are not met because gnomAD grpmax filtering AF is far below their VCEP thresholds.

BS2 is not applicable under the ATM VCEP because ATM has incomplete penetrance.

PM2 is not met because the highest all-comers gnomAD subpopulation frequency exceeds the VCEP threshold and the single-allele exception is not satisfied.

Met · 1

BP4 SupportingMet at supporting: SpliceAI maximum delta 0.059 meets the ATM VCEP BP4 splicing threshold of <=0.1. Details ▾Hide ▴

Reasoning

The variant is intronic at c.2377-18T>C with protein consequence p.?; therefore the applicable computational path is SpliceAI, not REVEL. SpliceAI reports a maximum delta score of 0.059, meeting the ATM VCEP Version 1.6 BP4 supporting threshold of <=0.1 for no predicted splice impact. BP4 is met at supporting strength. The governing ATM Table S1 file was searched for c.2377-18T>C, c.2377-18, 2377-18, and p.?; no exact entry was found, so it does not provide a pre-assigned BP4 code.

Rule

ATM VCEP Version 1.6 BP4 splicing: no predicted impact via SpliceAI <=0.1.

Evidence considered

ClinGen HBOP ATM VCEP Version 1.6 assigns BP4 Supporting for splicing when SpliceAI is <=0.1; the variant is intronic and therefore uses the SpliceAI path.
The case SpliceAI result reports DS_AG 0.007, DS_AL 0.059, DS_DG 0.000, and DS_DL 0.055, with maximum delta 0.059.
The governing Suppl_TableS1_PMID 40580951 full-text conversion was searched for c.2377-18T>C, c.2377-18, 2377-18, and p.?; no exact entry was found, so no pre-assigned BP4 code was available from that file.

Still missing

No exact entry for c.2377-18T>C, c.2377-18, 2377-18, or p.? was found in /Users/gs_agent/LYFESCI_HERMES_v9/vcep_db/ATM/fulltext/Suppl_TableS1_PMID 40580951.xlsx.txt.
No exact entry for c.2377-18T>C, c.2377-18, 2377-18, or p.? was found in /Users/gs_agent/LYFESCI_HERMES_v9/vcep_db/ATM/fulltext/clingen_hbop_atm_supplementary_tables_1_and_2_v1.xlsx.txt.

Sources

cspec ↗spliceai ↗vcep_suppl_tables1_pmid_40580951

Not met · 5 · evaluated, threshold not reached

PVS1 Not met: the intronic -18 variant is outside canonical splice positions, lacks RNA evidence, and has SpliceAI maximum delta 0.059. Details ▾Hide ▴

Reasoning

The ATM HBOP VCEP PVS1 guide applies to null variants, including canonical +/-1 or +/-2 splice variants, and to observed splice defects under its PVS1(RNA) pathway. NM_000051.4:c.2377-18T>C is an intronic variant at -18, outside the canonical -1/-2 splice positions; the case reports no observed RNA defect, and SpliceAI predicts no significant splice impact (maximum delta 0.059). Therefore, this variant does not meet the VCEP-defined PVS1 null-variant or observed-splice-defect criteria. The governing ATM_PVS1_1.5.pdf full text contains no entry keyed to c.2377-18T>C or p.?.

Rule

ATM HBOP VCEP PVS1/PVS1(RNA) decision guide: null variants and observed splice defects; canonical +/-1 or +/-2 splice positions are included, but this -18 intronic variant has no observed RNA defect and no significant SpliceAI prediction.

Evidence considered

The ATM HBOP VCEP PVS1 specification defines eligibility for null variants including canonical +/-1 or +/-2 splice variants and provides a separate PVS1(RNA) pathway for observed splice defects.
The assessed variant is NM_000051.4:c.2377-18T>C with protein annotation NP_000042.3:p.?, placing it 18 bases upstream of the coding exon rather than at a canonical +/-1 or +/-2 splice position.
SpliceAI reports a maximum delta score of 0.059, below the VCEP splicing-impact threshold of 0.2, with no significant predicted splice impact.
A direct search of ATM_PVS1_1.5.pdf.txt found no variant-specific entry for c.2377-18T>C or p.? .

Sources

cspec ↗spliceai ↗vcep_atm_pvs1_1_5

PM2 Not met: gnomAD v4.1 East Asian AF is 2.2346e-05 (0.00223%), above the ATM VCEP PM2 threshold of <=0.001%. Details ▾Hide ▴

Reasoning

The governing ATM VCEP v1.6 permits PM2_Supporting only when the frequency is <=0.001% in the gnomAD subpopulation with the highest frequency, with an exception for a single allele confined to one subpopulation. In the default all-comers datasets, the highest subpopulation frequency is 2.23463687150838e-05 in gnomAD v4.1 East Asians (1/44750; 0.00223%), which exceeds 0.001%, and the allele is also observed in other subpopulations; the single-allele exception therefore does not apply. gnomAD v2.1 likewise has a highest subpopulation frequency of 3.5245396070138335e-05 (4/113490; 0.00352%). The ATM specification does not require a non-cancer-only population source, so the default all-comers totals govern.

Rule

Frequency <=0.001% in gnomAD subpopulation with the highest frequency; exception if >0.001% but n=1 in a single subpopulation and absent from all other subpopulations

Evidence considered

ATM VCEP v1.6 specifies PM2_Supporting at frequency <=0.001% in the gnomAD subpopulation with the highest frequency, with a narrow exception for one allele confined to one subpopulation.
gnomAD v4.1 reports the highest subpopulation AF as 2.23463687150838e-05 in East Asians (1/44750; 0.00223%); the variant is also present in other subpopulations.
gnomAD v2.1 reports the highest subpopulation AF as 3.5245396070138335e-05 in European non-Finnish individuals (4/113490; 0.00352%).
The ATM specification does not require a non-cancer-only population source for PM2, so the default all-comers gnomAD datasets are used.

Sources

cspec ↗gnomad_v2 ↗gnomad_v4 ↗

PP3 Not met: SpliceAI maximum delta 0.059 is below the ATM VCEP PP3 splicing threshold of >=0.2. Details ▾Hide ▴

Reasoning

The variant is intronic at c.2377-18T>C with protein consequence p.?; therefore the applicable computational path is SpliceAI, not REVEL. SpliceAI reports a maximum delta score of 0.059, below the ATM VCEP Version 1.6 splicing PP3 supporting threshold of >=0.2, so PP3 is not met. The governing ATM Table S1 file was searched for c.2377-18T>C, c.2377-18, 2377-18, and p.?; no exact entry was found, so it does not provide a pre-assigned PP3 code.

Rule

ATM VCEP Version 1.6 PP3 splicing: SpliceAI >=0.2 for silent, missense/in-frame, and intronic variants outside donor/acceptor +/-1,2 sites.

Evidence considered

ClinGen HBOP ATM VCEP Version 1.6 assigns PP3 Supporting for splicing when SpliceAI is >=0.2; the variant is intronic and therefore uses the SpliceAI path.
The case SpliceAI result reports DS_AG 0.007, DS_AL 0.059, DS_DG 0.000, and DS_DL 0.055, with maximum delta 0.059.
The governing Suppl_TableS1_PMID 40580951 full-text conversion was searched for c.2377-18T>C, c.2377-18, 2377-18, and p.?; no exact entry was found, so no pre-assigned PP3 code was available from that file.

Still missing

No exact entry for c.2377-18T>C, c.2377-18, 2377-18, or p.? was found in /Users/gs_agent/LYFESCI_HERMES_v9/vcep_db/ATM/fulltext/Suppl_TableS1_PMID 40580951.xlsx.txt.
No exact entry for c.2377-18T>C, c.2377-18, 2377-18, or p.? was found in /Users/gs_agent/LYFESCI_HERMES_v9/vcep_db/ATM/fulltext/clingen_hbop_atm_supplementary_tables_1_and_2_v1.xlsx.txt.

Sources

cspec ↗spliceai ↗vcep_suppl_tables1_pmid_40580951

BA1 Not met: gnomAD v4.1 grpmax filtering AF is 5.49e-06, below the ATM VCEP BA1 threshold of >0.005. Details ▾Hide ▴

Reasoning

The governing ATM VCEP v1.6 defines BA1 as grpmax filtering AF >0.5% in gnomAD. The observed grpmax filtering AF is 1.123e-05 in gnomAD v2.1 and 5.49e-06 in gnomAD v4.1, both far below 0.005; therefore BA1 is not met.

Rule

Grpmax Filtering AF >0.5% in gnomAD

Evidence considered

ATM VCEP v1.6 specifies BA1 for grpmax filtering AF >0.5% (>0.005) in gnomAD.
gnomAD v2.1 reports grpmax filtering AF 1.123e-05; gnomAD v4.1 reports grpmax filtering AF 5.49e-06.
Neither population frequency reaches the governing BA1 threshold.

Sources

cspec ↗gnomad_v2 ↗gnomad_v4 ↗

BS1 Not met: gnomAD v4.1 grpmax filtering AF is 5.49e-06, below the ATM VCEP BS1 threshold of >0.0005. Details ▾Hide ▴

Reasoning

The governing ATM VCEP v1.6 defines BS1 as grpmax filtering AF >0.05% in gnomAD. The observed grpmax filtering AF is 1.123e-05 in gnomAD v2.1 and 5.49e-06 in gnomAD v4.1, both below 0.0005; therefore BS1 is not met.

Rule

Grpmax Filtering AF >0.05% in gnomAD

Evidence considered

ATM VCEP v1.6 specifies BS1 for grpmax filtering AF >0.05% (>0.0005) in gnomAD.
gnomAD v2.1 reports grpmax filtering AF 1.123e-05; gnomAD v4.1 reports grpmax filtering AF 5.49e-06.
Neither population frequency reaches the governing BS1 threshold.

Sources

cspec ↗gnomad_v2 ↗gnomad_v4 ↗

Not assessed · 7 · no assessment recorded

PS1 Not assessed: SpliceAI max delta is 0.059, but no qualifying same-event P/LP reference entry was found for PS1 comparison. Details ▾Hide ▴

Reasoning

The variant is intronic (NM_000051.4:c.2377-18T>C; NP_000042.3:p.?), so the ATM PS1 splicing path is the applicable VCEP path. ATM_PS1_1.5.pdf requires a known P/LP reference variant with the same predicted splice event and comparable or greater prediction strength, but searches of the complete file found no entry for c.2377-18T>C or p.?. The case has SpliceAI max delta 0.059, but no qualifying reference event is available for comparison; therefore PS1 cannot be assigned.

Rule

ATM VCEP PS1 splicing path: apply only with the same predicted splice event as a known (likely) pathogenic reference variant and prediction strength equal to or greater than the reference.

Evidence considered

The ATM VCEP framework states that splice-region PS1 requires use of the ATM PS1 splicing table and that the variant-under-assessment and reference variant must have precisely matching predicted splice events, with prediction strength for the assessed variant equal to or greater than the reference.
The complete ATM_PS1_1.5.pdf text was searched for c.2377-18T>C and p.?; neither notation was found, so no governing pre-assigned code applies to this variant.
SpliceAI reports a maximum delta score of 0.059 for NM_000051.4:c.2377-18T>C, without a documented qualifying P/LP comparator in the governing PS1 table.

Still missing

ATM_PS1_1.5.pdf contains no entry for c.2377-18T>C or p.?; a qualifying P/LP reference variant with the same predicted splice event and comparable prediction strength is not available.

Sources

cspec ↗vcep_atm_ps1_1_5spliceai ↗

PS3 Not assessed: no variant-specific ATM kinase or radiosensitivity result was found in the governing approved-assay sources for c.2377-18T>C. Details ▾Hide ▴

Reasoning

The ATM VCEP Version 1.6 specifies PS3 Supporting when a variant fails to rescue an ATM-specific feature such as phosphorylation of ATM-specific targets, and PS3 Moderate only when it fails to rescue both an ATM-specific feature and radiosensitivity; radiosensitivity alone receives no weight. The governing approved-assay table is a methodology and calibration table, not a per-variant results table, and requires confirmation that the variant was tested in Mitui 2009 (PMID:18634022), Barone 2009 (PMID:19431188), or Scott 2002 (PMID:11805335). Exact searches of that table and the available case evidence found no result for NM_000051.4:c.2377-18T>C, c.2377-18T>C, or p.?. Exact searches of Sun et al. 2025 Table S1 (PMID:40580951) likewise found no c.2377-18T>C entry. Therefore no qualifying variant-specific functional assay result is available to assign PS3, and the criterion is not assessed rather than treated as absent functional evidence.

Rule

ATM VCEP Version 1.6 PS3: do not use Strong; Moderate requires failure to rescue both an ATM-specific feature and radiosensitivity; Supporting requires failure to rescue an ATM-specific feature only; radiosensitivity alone receives no weight.

Evidence considered

ClinGen HBOP ATM VCEP Version 1.6: PS3 Strong is prohibited; PS3 Moderate requires failure to rescue both an ATM-specific feature and radiosensitivity, while PS3 Supporting applies to failure to rescue an ATM-specific feature only and not to radiosensitivity alone.
The governing ATM functional-assay table lists Mitui 2009 (PMID:18634022), Barone 2009 (PMID:19431188), and Scott 2002 (PMID:11805335) as approved kinase-activity assays, but explicitly states that it is not a per-variant results table and requires confirmation that the assessed variant was tested.
The governing approved-assay table was searched for c.2377-18T>C and p.?; no matching variant entry was found.
Sun et al. 2025 Table S1 was searched for c.2377-18T>C; no matching row was found, so no DeepATM_predicted status or direct functional classification can be assigned for this variant from that table.

Still missing

No entry for c.2377-18T>C, c.2377-18T>C, or p.? was found in clingen_hbop_atm_supplementary_tables_1_and_2_v1.xlsx; this file is a calibration table rather than a per-variant results table.
No entry for c.2377-18T>C was found in Suppl_TableS1_PMID 40580951.xlsx.txt.
Variant-specific assay reports for Mitui 2009 (PMID:18634022), Barone 2009 (PMID:19431188), and Scott 2002 (PMID:11805335) were not present in the case evidence and were not confirmed as having tested this variant.

Sources

cspec ↗vcep_clingen_hbop_atm_supplementary_tables_1_and_2_v1vcep_suppl_tables1_pmid_40580951

PS4 Not assessed: no variant-specific case-control p-value, effect estimate, or confidence interval is available to evaluate the ATM PS4 thresholds. Details ▾Hide ▴

Reasoning

The ATM VCEP v1.6 specification makes PS4 applicable at Strong strength only for case-control studies with p-value <=0.05 and either an odds ratio, hazard ratio, or relative risk >=2 or a lower 95% confidence interval >=1.5. No case-control study, p-value, effect estimate, confidence interval, or qualifying affected-case/control comparison for NM_000051.4:c.2377-18T>C is documented in the available evidence. The variant-specific literature extractions do not identify this variant in a phenotype or prevalence study, so PS4 cannot be adjudicated.

Rule

Case-control studies; p-value <=.05 and (Odds ratio, hazard ratio, or relative risk >=2 or lower 95% CI >=1.5). PS4_Moderate is not used by this VCEP.

Evidence considered

ATM VCEP v1.6 states: "Case-control studies; p-value <=.05 and (Odds ratio, hazard ratio, or relative risk >=2 or lower 95% CI >=1.5)."
No exact-variant case-control prevalence or enrichment result is present in the reviewed evidence.

Still missing

A variant-specific case-control study or calibrated affected-case/control dataset with p-value and odds ratio, hazard ratio, relative risk, or lower 95% confidence interval is needed.

Sources

cspec ↗

PM3 Not assessed: no affected-proband, homozygous, second-allele, or phase evidence is available to assign the ATM VCEP's PM3 points. Details ▾Hide ▴

Reasoning

The governing ClinGen HBOP ATM PM3/BP2 specification requires affected A-T proband observations with the variant homozygous, in trans with a pathogenic/likely pathogenic ATM variant, phase unknown, or with an unidentified/VUS second variant, and assigns points from the documented phenotype and phase. The case evidence contains no affected-proband observation, second ATM allele, phase result, or qualifying homozygous A-T case for NM_000051.4:c.2377-18T>C (NP_000042.3:p.?). The variant was searched in ATM_PM3_BP2_1.5.pdf under c.2377-18T>C and p.?; no variant-specific entry was found, so no PM3 points or strength can be assigned.

Rule

ATM VCEP PM3: assign points per unrelated A-T proband according to phenotype and phase/zygosity; PM3 Supporting=1.0, Moderate=2.0, Strong=4.0, Very Strong=8.0 points.

Evidence considered

ATM_PM3_BP2_1.5.pdf specifies PM3 for recessive A-T using affected-proband observations and phase/zygosity-specific points: confident phenotype is worth 4.0 points confirmed in trans, 2.0 phase unknown, 1.0 with an unidentified/VUS second variant, or 2.0 for homozygous observations; consistent phenotype receives half those values.
The consolidated case evidence identifies the variant as NM_000051.4:c.2377-18T>C with protein annotation NP_000042.3:p.? but provides no affected-proband, second-allele, phase, or homozygous A-T observation applicable to PM3.
The notation c.2377-18T>C and p.? was searched in ATM_PM3_BP2_1.5.pdf; no variant-specific table entry was found.

Still missing

No entry for NM_000051.4:c.2377-18T>C, c.2377-18T>C, or p.? was found in ATM_PM3_BP2_1.5.pdf.
Affected-proband observations and A-T phenotype classification are unavailable.
A qualifying pathogenic/likely pathogenic ATM allele in trans, phase information, or qualifying homozygous A-T observations are unavailable.

Sources

vcep_atm_pm3_bp2_1_5

PP1 Not assessed: no affected-relative segregation, parental testing, phase, or meiosis data are documented to meet the ATM PP1 thresholds. Details ▾Hide ▴

Reasoning

The ATM VCEP version 1.6 permits PP1 only for autosomal-recessive disease, with Supporting assigned for segregation in one affected relative, Moderate for two, and Strong for at least three. The available case evidence contains no documented affected relative, parental testing result, phase information, or meiosis count for this variant, so segregation cannot be assessed.

Rule

AR Condition: Segregation in 1 affected relative = Supporting; segregation in 2 affected relatives = Moderate; segregation in 3 or more affected relatives = Strong.

Evidence considered

ATM VCEP v1.6 defines PP1 for the autosomal-recessive condition as Supporting for segregation in one affected relative, Moderate for two, and Strong for at least three.
No variant-specific affected-relative, parental-testing, phase, or meiosis data are documented in the reviewed case evidence.

Still missing

Documented affected relatives carrying the variant and their ATM-related phenotype
Parental testing and phase information
Number of informative meioses or segregations

Sources

cspec ↗

BS3 Not assessed: no variant-specific ATM rescue or normal-function result was found in the governing approved-assay sources for c.2377-18T>C. Details ▾Hide ▴

Reasoning

The ATM VCEP Version 1.6 specifies BS3 Supporting when a variant rescues either an ATM-specific feature or radiosensitivity, and BS3 Moderate when it rescues both. The governing approved-assay table is a methodology and strength-calibration table, not a per-variant results table; its kinase assays require variant-specific confirmation in Mitui 2009 (PMID:18634022), Barone 2009 (PMID:19431188), or Scott 2002 (PMID:11805335), and radiosensitivity cannot be used alone. Exact searches of the governing table and the available case evidence found no result for NM_000051.4:c.2377-18T>C, c.2377-18T>C, or p.?. Exact searches of Sun et al. 2025 Table S1 (PMID:40580951) found no c.2377-18T>C entry. Thus no qualifying variant-specific normal-function or rescue result is available to assign BS3, and the criterion is not assessed rather than treated as evidence of benign function.

Rule

ATM VCEP Version 1.6 BS3: Moderate requires rescue of both an ATM-specific feature and radiosensitivity; Supporting applies when either an ATM-specific feature or radiosensitivity is rescued.

Evidence considered

ClinGen HBOP ATM VCEP Version 1.6: BS3 Moderate requires rescue of both an ATM-specific feature and radiosensitivity; BS3 Supporting applies when either an ATM-specific feature or radiosensitivity is rescued.
The governing ATM functional-assay table lists approved kinase-activity methodology and calibrated strengths, but explicitly states that it is not a per-variant results table and that radiosensitivity alone receives no weight.
The governing approved-assay table was searched for c.2377-18T>C and p.?; no matching variant entry was found.
Sun et al. 2025 Table S1 was searched for c.2377-18T>C; no matching row was found, so no direct normal-function result is available for this variant from that table.

Still missing

No entry for c.2377-18T>C, c.2377-18T>C, or p.? was found in clingen_hbop_atm_supplementary_tables_1_and_2_v1.xlsx; this file is a calibration table rather than a per-variant results table.
No entry for c.2377-18T>C was found in Suppl_TableS1_PMID 40580951.xlsx.txt.
Variant-specific assay reports for Mitui 2009 (PMID:18634022), Barone 2009 (PMID:19431188), and Scott 2002 (PMID:11805335) were not present in the case evidence and were not confirmed as having tested this variant.

Sources

cspec ↗vcep_clingen_hbop_atm_supplementary_tables_1_and_2_v1vcep_suppl_tables1_pmid_40580951

BP2 Not assessed: no unaffected adult carrying this variant with a pathogenic ATM allele in trans or qualifying homozygous observation is documented. Details ▾Hide ▴

Reasoning

The governing ClinGen HBOP ATM PM3/BP2 specification requires unaffected non-A-T adults carrying the variant with a pathogenic/likely pathogenic ATM variant in trans, with separate weights for confirmed trans, phase unknown, or laboratory/database-setting homozygous observations. The case evidence contains no unaffected adult observation, co-occurring pathogenic/likely pathogenic ATM variant, phase result, or qualifying homozygous individual for NM_000051.4:c.2377-18T>C (NP_000042.3:p.?). The variant was searched in ATM_PM3_BP2_1.5.pdf under c.2377-18T>C and p.?; no variant-specific entry was found, so no BP2 points or strength can be assigned.

Rule

ATM VCEP BP2: assign negative points per unaffected non-A-T adult with a pathogenic/likely pathogenic ATM variant according to phase and laboratory/database setting; BP2 Supporting=-1.0, Moderate=-2.0, Strong≤-4.0 points.

Evidence considered

ATM_PM3_BP2_1.5.pdf specifies BP2 for unaffected non-A-T adults carrying the variant with a pathogenic or likely pathogenic ATM variant: -4.0 points confirmed in trans, -2.0 points phase unknown, and homozygous observations weighted -2.0 in a laboratory setting or -1.0 in a database setting, with a maximum homozygous contribution of -2.0.
The consolidated case evidence identifies the variant as NM_000051.4:c.2377-18T>C with protein annotation NP_000042.3:p.? but provides no unaffected-adult, co-occurring ATM allele, phase, or qualifying homozygous observation applicable to BP2.
The notation c.2377-18T>C and p.? was searched in ATM_PM3_BP2_1.5.pdf; no variant-specific table entry was found.

Still missing

No entry for NM_000051.4:c.2377-18T>C, c.2377-18T>C, or p.? was found in ATM_PM3_BP2_1.5.pdf.
Unaffected non-A-T adult observations are unavailable.
A qualifying pathogenic/likely pathogenic ATM allele in trans, phase information, and laboratory/database-setting details are unavailable.

Sources

vcep_atm_pm3_bp2_1_5

Not applicable · 15· recorded as not applicable Show reasons ▾Hide reasons ▴

PS2 VCEPNot applicable: the ATM VCEP v1.6 explicitly excludes PS2 for autosomal-dominant and autosomal-recessive ATM disease. Details ▾Hide ▴

Reasoning

The ClinGen HBOP ATM VCEP version 1.6 specification marks PS2 as not applicable and instructs that informative de novo occurrences have not been observed for ATM autosomal-dominant or autosomal-recessive disease; therefore no PS2 evidence is assigned.

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 marks PS2 as not applicable and states that informative de novo occurrences have not been observed for ATM autosomal-dominant or autosomal-recessive disease.

Sources

cspec ↗

PM1 VCEPNot applicable: ATM VCEP marks PM1 not applicable, and this intronic variant has protein consequence p.? rather than a codon residue. Details ▾Hide ▴

Reasoning

The ATM Version 1.6 VCEP marks PM1 as Not Applicable. The variant is intronic and has protein consequence p.?, so it does not encode a residue that can be evaluated against a missense critical-domain list. vcep_materials.json has no ATM domain_tables entry.

VCEP rule

ATM VCEP PM1: Not Applicable.

Evidence considered

The ATM Version 1.6 VCEP framework explicitly marks PM1 as Not Applicable.
The case normalization is NM_000051.4:c.2377-18T>C with NP_000042.3:p.?, and vcep_materials.json contains an empty domain_tables object for ATM.

Sources

cspec ↗

PM4 N/ANot applicable: PM4 is reserved for stop-loss variants, whereas this intronic variant has protein annotation p.? and no protein-length change. Details ▾Hide ▴

Reasoning

The ATM VCEP specification limits PM4 to stop-loss variants. NM_000051.4:c.2377-18T>C is an intronic variant with protein annotation NP_000042.3:p.? and is not a stop-loss or protein-length-changing variant; PM4 is therefore not applicable.

Rule

ATM VCEP PM4: use for stop-loss variants only.

Evidence considered

The ATM VCEP Version 1.6 rule for PM4 states: use for stop-loss variants.
The assessed variant is intronic, NM_000051.4:c.2377-18T>C, with protein annotation NP_000042.3:p.?, so no stop-loss or protein-length change is established.

Sources

cspec ↗

PM5 N/ANot applicable: ATM PM5 is restricted to qualifying truncating or observed NMD-prone splice variants, whereas this variant is c.2377-18T>C with p.?. Details ▾Hide ▴

Reasoning

The ATM Version 1.6 VCEP PM5 rule is restricted to specified NMD-prone truncating or observed NMD-prone splice variants receiving PVS1 at Very Strong with a premature termination codon upstream of p.Leu3048. This variant is intronic with protein consequence p.? and is not a qualifying truncating comparator scenario; classic same-residue missense PM5 is not applicable.

Rule

ATM VCEP PM5: apply only to the specified truncation/NMD-prone splice scenarios; not classic same-residue missense PM5.

Evidence considered

The ATM Version 1.6 VCEP specifies PM5 only for qualifying NMD-prone truncating variants or observed NMD-prone splice variants with PVS1(RNA) Very Strong and a premature termination codon upstream of p.Leu3048.
The case PM5 candidate summary identifies the governing mode as truncation-cutoff_gene-specific and reports no eligible classic same-residue missense search candidates.

Sources

cspec ↗pm5_candidates

PM6 VCEPNot applicable: the ATM VCEP v1.6 explicitly excludes PM6 for autosomal-dominant and autosomal-recessive ATM disease. Details ▾Hide ▴

Reasoning

The ClinGen HBOP ATM VCEP version 1.6 specification marks PM6 as not applicable and instructs that assumed de novo evidence should not be used for ATM autosomal-dominant or autosomal-recessive disease; therefore no PM6 evidence is assigned.

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 marks PM6 as not applicable and states that assumed de novo evidence should not be used for ATM autosomal-dominant or autosomal-recessive disease.

Sources

cspec ↗

PP2 VCEPNot applicable: ATM VCEP marks PP2 not applicable, and the variant is intronic with protein consequence p.? rather than missense. Details ▾Hide ▴

Reasoning

The ATM Version 1.6 VCEP explicitly marks PP2 as Not Applicable. In addition, this variant is intronic with protein consequence p.?, so a gene-level missense-enrichment criterion cannot be applied.

VCEP rule

ATM VCEP PP2: Not Applicable.

Evidence considered

The ATM Version 1.6 VCEP framework explicitly marks PP2 as Not Applicable.
The case normalization identifies c.2377-18T>C as intronic with NP_000042.3:p.?, not a missense substitution.

Sources

cspec ↗

PP4 VCEPNot applicable: the ATM VCEP prohibits separate PP4 use for both ATM-related cancer predisposition and ataxia-telangiectasia. Details ▾Hide ▴

Reasoning

The ATM VCEP v1.6 explicitly marks PP4 not applicable. For autosomal dominant ATM-related cancer predisposition, breast cancer has genetic heterogeneity and no phenotype features readily distinguish hereditary from sporadic causes; for autosomal recessive ataxia-telangiectasia, phenotype evidence is incorporated into the ATM PM3/BP2 framework rather than used as a separate PP4 line of evidence.

VCEP rule

Autosomal dominant: do not use because breast cancer is genetically heterogeneous and lacks a readily distinguishing phenotype. Autosomal recessive: do not use as a separate line of evidence; phenotype evidence is incorporated into the ATM PM3/BP2 table.

Evidence considered

ATM VCEP v1.6 marks PP4 "Not applicable" and instructs that it must not be used separately for autosomal dominant ATM-related cancer or autosomal recessive ataxia-telangiectasia.

Sources

cspec ↗

PP5 VCEPNot applicable: ATM prohibits PP5, and ClinVar has no exact-variant expert-panel Pathogenic or Likely pathogenic classification. Details ▾Hide ▴

Reasoning

The ATM VCEP v1.6 marks PP5 not applicable and states that it is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. In addition, the exact-variant ClinVar record has no expert-panel submission; it contains only five clinical-laboratory Likely benign submissions, so it does not meet the required exact-variant expert-panel Pathogenic or Likely pathogenic trigger for PP5.

VCEP rule

Do not use PP5 under the ATM VCEP. Under the requested expert-panel-only policy, PP5 would require an exact-variant ClinVar Expert Panel Pathogenic or Likely pathogenic classification.

Evidence considered

ATM VCEP v1.6 states: "This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee."
The exact-variant ClinVar record reports five clinical-laboratory Likely benign submissions and zero expert-panel submissions; ordinary laboratory submissions do not trigger PP5.

Sources

cspec ↗clinvar ↗

BS2 VCEPNot applicable: the ATM VCEP excludes BS2 because ATM-related disease has incomplete penetrance. Details ▾Hide ▴

Reasoning

The governing ATM VCEP v1.6 explicitly designates BS2 as not applicable because ATM has incomplete penetrance. Population observations in gnomAD therefore cannot establish BS2 for this variant under the governing specification.

VCEP rule

Do not use: ATM has incomplete penetrance.

Evidence considered

ATM VCEP v1.6 states: do not use BS2 because ATM has incomplete penetrance.

Sources

cspec ↗

BS4 VCEPNot applicable: the ATM VCEP v1.6 excludes BS4 because informative non-segregation in ataxia-telangiectasia families is too rare. Details ▾Hide ▴

Reasoning

The ClinGen HBOP ATM VCEP version 1.6 specification marks BS4 as not applicable. It states that informative lack-of-segregation instances in ataxia-telangiectasia families are too rare to receive weight at this time, so no BS4 evidence is assigned.

VCEP rule

AR Condition: Informative instances of lack of co-segregation in A-T families are too rare to be considered for weight at this time.

Evidence considered

ATM VCEP v1.6 marks BS4 as not applicable and states that informative lack-of-segregation instances in ataxia-telangiectasia families are too rare for weight.

Sources

cspec ↗

BP1 VCEPNot applicable: ATM VCEP marks BP1 not applicable, and this variant is intronic with protein consequence p.? rather than missense. Details ▾Hide ▴

Reasoning

The ATM Version 1.6 VCEP explicitly marks BP1 as Not Applicable. The variant is intronic with protein consequence p.?, so the generic benign criterion for a missense variant in a gene where missense is not a common disease mechanism does not apply.

VCEP rule

ATM VCEP BP1: Not Applicable.

Evidence considered

The ATM Version 1.6 VCEP framework explicitly marks BP1 as Not Applicable.
The case normalization identifies c.2377-18T>C as intronic with NP_000042.3:p.?, not a missense substitution.

Sources

cspec ↗

BP3 VCEPNot applicable: the ATM VCEP explicitly designates BP3 as Not Applicable for this framework. Details ▾Hide ▴

Reasoning

The ATM HBOP VCEP specification explicitly marks BP3 as Not Applicable. The governing VCEP rule therefore takes precedence over generic ACMG/AMP consideration of an in-frame deletion or repeat-region context, and BP3 is not applicable to this variant.

VCEP rule

ATM HBOP VCEP Version 1.6: BP3 is Not Applicable.

Evidence considered

The ATM HBOP VCEP Version 1.6 criterion table explicitly lists BP3 applicability as Not Applicable.
No generic BP3 assessment can override the governing ATM VCEP specification.

Sources

cspec ↗

BP5 VCEPNot applicable: the ATM VCEP prohibits BP5 because co-occurring pathogenic variants are common and may not alter the phenotype. Details ▾Hide ▴

Reasoning

The ATM VCEP v1.6 explicitly marks BP5 not applicable and instructs that it must not be used because multiple pathogenic variants can occur without a noticeable phenotype difference, while ATM's low penetrance increases the likelihood of co-occurring pathogenic variants. No alternate molecular basis can therefore be converted into BP5 under this governing specification.

VCEP rule

Do not use BP5 under the ATM VCEP.

Evidence considered

ATM VCEP v1.6 states: "Do not use: Cases with multiple pathogenic variants have been observed with no noticeable difference in phenotype ... ATM has low penetrance and will naturally occur with other pathogenic variants more frequently."

Sources

cspec ↗

BP6 VCEPNot applicable: ATM prohibits BP6, and ClinVar has no exact-variant expert-panel Benign or Likely benign classification. Details ▾Hide ▴

Reasoning

The ATM VCEP v1.6 marks BP6 not applicable and states that it is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. The exact-variant ClinVar record has no expert-panel submission and only ordinary clinical-laboratory Likely benign submissions; therefore it does not meet the required exact-variant expert-panel Benign or Likely benign trigger for BP6.

VCEP rule

Do not use BP6 under the ATM VCEP. Under the requested expert-panel-only policy, BP6 would require an exact-variant ClinVar Expert Panel Benign or Likely benign classification.

Evidence considered

ATM VCEP v1.6 states: "This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee."
The exact-variant ClinVar record reports five clinical-laboratory Likely benign submissions and zero expert-panel submissions; ordinary laboratory submissions do not trigger BP6.

Sources

cspec ↗clinvar ↗

BP7 N/ANot applicable: c.2377-18T>C is intronic, whereas BP7 applies only to synonymous variants. Details ▾Hide ▴

Reasoning

BP7 is restricted to synonymous variants under the requested scope. This variant is intronic (c.2377-18T>C; p.?), not synonymous, so BP7 is not applicable and no predictor score is evaluated for BP7.

Rule

BP7 applies only to synonymous variants under the requested criterion scope.

Evidence considered

The ATM VCEP Version 1.6 BP7 rule is scoped to synonymous and deep intronic variants, while the requested criterion scope restricts BP7 to synonymous variants only.
The case normalization identifies c.2377-18T>C as intronic with protein consequence p.?.

Sources

cspec ↗

Identifiers

Gene: ATM
Transcript: NM_000051.4
Coding (HGVS c.): NM_000051.4:c.2377-18T>C
Protein (HGVS p.): NP_000042.3:p.?
GRCh38: chr11:108258968 T>C
GRCh37: chr11:108129695 T>C
Location and type: Intron 15 · unknown
ClinVar: 381894

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…

Exons

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Transcript span

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Strand

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Variants mapped

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Source

UCSC ncbiRefSeqCurated

All variants in ATM — Select a row to find it on the plot; use the link to open its page.

	Protein	Location	Classification	Link

gnomAD v4.1 15 / 1,597,506 alleles AF 9.39e-06 · 0 homozygotes · FAF 5.49e-06

gnomAD v2.1 5 / 250,866 alleles AF 1.99e-05 · 0 homozygotes · FAF 1.12e-05

gnomAD-Canada v1.0 Allele count data not recorded

By genetic ancestry

gnomAD v4.1

AF 9.4e-06 · 15 / 1,597,506 alleles · 0 hom · FAF 5.5e-06

East Asian1 / 44,750	2.2e-05
Remaining individuals1 / 61,932	1.6e-05
South Asian1 / 90,724	1.1e-05
European (non-Finnish)12 / 1,165,318	1e-05

0 alternate alleles recorded in 6 other groups: Admixed American, European (Finnish), Amish, Middle Eastern, Ashkenazi Jewish, African/African American.

gnomAD v2.1

AF 2e-05 · 5 / 250,866 alleles · 0 hom · FAF 1.1e-05

European (non-Finnish)4 / 113,490	3.5e-05
South Asian1 / 30,554	3.3e-05

0 alternate alleles recorded in 6 other groups: African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals.

Statements

gnomAD v4.1

This variant is present in gnomAD v4.1 (AF= 9.38964e-06; MAF= 0.00094%, 15/1597506 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 2.23464e-05; MAF= 0.00223%, 1/44750 alleles, homozygotes = 0); grpmax FAF= 5.49e-06.

gnomAD v2.1

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

SpliceAI and Pangolin

SpliceAI acceptor lossat +21 bp

0.059

SpliceAI acceptor gainat -59 bp

0.007

SpliceAI donor lossat +107 bp

0.055

SpliceAI donor gainat -7 bp

0.000

Pangolin splice lossmagnitude shown

-0.035

Pangolin splice gain

0.004

Other predictors

REVEL: Not available
BayesDel: Not available

How the predictions were used

BP4 SupportingMet at supporting: SpliceAI maximum delta 0.059 meets the ATM VCEP BP4 splicing threshold of <=0.1. Details ▾Hide ▴

Reasoning

Rule

ATM VCEP Version 1.6 BP4 splicing: no predicted impact via SpliceAI <=0.1.

Evidence considered

ClinGen HBOP ATM VCEP Version 1.6 assigns BP4 Supporting for splicing when SpliceAI is <=0.1; the variant is intronic and therefore uses the SpliceAI path.
The case SpliceAI result reports DS_AG 0.007, DS_AL 0.059, DS_DG 0.000, and DS_DL 0.055, with maximum delta 0.059.
The governing Suppl_TableS1_PMID 40580951 full-text conversion was searched for c.2377-18T>C, c.2377-18, 2377-18, and p.?; no exact entry was found, so no pre-assigned BP4 code was available from that file.

Still missing

No exact entry for c.2377-18T>C, c.2377-18, 2377-18, or p.? was found in /Users/gs_agent/LYFESCI_HERMES_v9/vcep_db/ATM/fulltext/Suppl_TableS1_PMID 40580951.xlsx.txt.
No exact entry for c.2377-18T>C, c.2377-18, 2377-18, or p.? was found in /Users/gs_agent/LYFESCI_HERMES_v9/vcep_db/ATM/fulltext/clingen_hbop_atm_supplementary_tables_1_and_2_v1.xlsx.txt.

Sources

cspec ↗spliceai ↗vcep_suppl_tables1_pmid_40580951

PP3 Not met: SpliceAI maximum delta 0.059 is below the ATM VCEP PP3 splicing threshold of >=0.2. Details ▾Hide ▴

Reasoning

The variant is intronic at c.2377-18T>C with protein consequence p.?; therefore the applicable computational path is SpliceAI, not REVEL. SpliceAI reports a maximum delta score of 0.059, below the ATM VCEP Version 1.6 splicing PP3 supporting threshold of >=0.2, so PP3 is not met. The governing ATM Table S1 file was searched for c.2377-18T>C, c.2377-18, 2377-18, and p.?; no exact entry was found, so it does not provide a pre-assigned PP3 code.

Rule

ATM VCEP Version 1.6 PP3 splicing: SpliceAI >=0.2 for silent, missense/in-frame, and intronic variants outside donor/acceptor +/-1,2 sites.

Evidence considered

ClinGen HBOP ATM VCEP Version 1.6 assigns PP3 Supporting for splicing when SpliceAI is >=0.2; the variant is intronic and therefore uses the SpliceAI path.
The case SpliceAI result reports DS_AG 0.007, DS_AL 0.059, DS_DG 0.000, and DS_DL 0.055, with maximum delta 0.059.
The governing Suppl_TableS1_PMID 40580951 full-text conversion was searched for c.2377-18T>C, c.2377-18, 2377-18, and p.?; no exact entry was found, so no pre-assigned PP3 code was available from that file.

Still missing

No exact entry for c.2377-18T>C, c.2377-18, 2377-18, or p.? was found in /Users/gs_agent/LYFESCI_HERMES_v9/vcep_db/ATM/fulltext/Suppl_TableS1_PMID 40580951.xlsx.txt.
No exact entry for c.2377-18T>C, c.2377-18, 2377-18, or p.? was found in /Users/gs_agent/LYFESCI_HERMES_v9/vcep_db/ATM/fulltext/clingen_hbop_atm_supplementary_tables_1_and_2_v1.xlsx.txt.

Sources

cspec ↗spliceai ↗vcep_suppl_tables1_pmid_40580951

BP7 N/ANot applicable: c.2377-18T>C is intronic, whereas BP7 applies only to synonymous variants. Details ▾Hide ▴

Reasoning

BP7 is restricted to synonymous variants under the requested scope. This variant is intronic (c.2377-18T>C; p.?), not synonymous, so BP7 is not applicable and no predictor score is evaluated for BP7.

Rule

BP7 applies only to synonymous variants under the requested criterion scope.

Evidence considered

The ATM VCEP Version 1.6 BP7 rule is scoped to synonymous and deep intronic variants, while the requested criterion scope restricts BP7 to synonymous variants only.
The case normalization identifies c.2377-18T>C as intronic with protein consequence p.?.

Sources

cspec ↗

Statement

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.06).

7 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.

No paper-specific finding is recorded.

PMID 25741868 ↗
Customizing local and systemic therapies for women with early breast cancer: the St. Gallen International Consensus Guidelines for treatment of early breast cancer 2021.

No paper-specific finding is recorded.

PMID 34242744 ↗
Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors.

Trepanier A et al. · 2004

No paper-specific finding is recorded.

PMID 15604628 ↗
The emerging landscape of breast cancer susceptibility.

Stratton MR et al. · 2008

No paper-specific finding is recorded.

PMID 18163131 ↗
BRCA1- and BRCA2-Associated Hereditary Breast and Ovarian Cancer.

Adam MP et al. · 1993

No paper-specific finding is recorded.

PMID 20301425 ↗
ACMG SF v3.0 list for reporting of secondary findings in clinical exome and genome sequencing: a policy statement of the American College of Medical Genetics and Genomics (ACMG).

No paper-specific finding is recorded.

PMID 34012068 ↗
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 15 / 1,597,506 recorded alleles Open source ↗

gnomAD v2.1 Captured gnomAD v2.1 source record Open source ↗

SpliceAI Lookup Recorded maximum delta 0.059 Open source ↗

ClinVar 5 Likely benign Open source ↗

COSMIC Captured COSMIC 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

gnomAD v2.1

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

ClinVar

This variant has been reported in ClinVar as Likely benign (5 clinical laboratories). (ClinVarID = 381894)

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.06).

Somatic

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