About ATM
No gene-level summary was recorded for this case.
Previous versions
Variant interpretation report
ATM c.5178-28T>A, p.?
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.
Words with a dotted underline have a short definition. Hover or tap them.
LYFE Sciences is an AI system, and it can make mistakes.
Criteria may be applied incorrectly, sources may be misread, and a
confident-looking classification can still be wrong.
Double-check every criterion and its underlying evidence
before relying on any call.
01The reasoning
How it was classified
The recorded framework is ClinGen ATM VCEP v1.5.0. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
Recorded applied criteria
The applied criteria and their strengths are shown as assessed under the stated framework.
Pathogenic evidence criteria: 2
Benign evidence criteria: 0
Pathogenic criteria applied · 2
PM2Supporting
PM2 · supporting
c.5178-28T>A is absent from all queried population databases: gnomAD v2.1 (exomes), gnomAD v4.1 (genomes+exomes), and gnomAD-Canada v1.0 (HostSeq genomes). Per the ATM VCEP 1.5.0, PM2_Supporting applies when the variant frequency is ≤0.001% in the gnomAD v4 dataset. Complete absence in >800,000 alleles satisfies this threshold.
PP3Supporting
PP3 · supporting
SpliceAI predicts a splicing impact for this intronic variant with a max delta score of 0.27 (DS_AL=0.27, DS_DL=0.26), exceeding the ATM VCEP 1.5.0 threshold of ≥0.2 for PP3. This criterion applies to intronic variants outside the donor and acceptor ±1,2 sites. The SpliceAI prediction suggests the variant may create an alternative splice acceptor or donor site. Per the VCEP, PP3 for splice predictions is applied at the Supporting strength level only.
Benign criteria applied · 0
No benign criterion marked as applied in the recorded assessment.
Recorded classification: Uncertain significance
Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting, PP3 supporting; no rule matched the adjudicated criteria.
02The sources
Evidence at a glance
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1
gnomAD v2.1
Population frequency
Not recorded
gnomAD v4.1 allele counts were not recorded for this variant.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI score
0.270 maximum delta
Recorded SpliceAI maximum delta score: 0.270. Refer to the recorded PP3/BP4 rationale for interpretation.
ClinVar submissions
Not recorded
A ClinVar laboratory submission summary was not recorded.
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 v1.5.0, with the data and sources behind each one.
29 criteria with recorded statuses: 2 met · 6 not met · 7 not assessed · 14 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Met
Not met
Not assessed
Not applicable
c.5178-28T>A is a rare deep intronic variant in ATM, located 28 bp upstream of the exon 35 acceptor splice site, that is absent from all queried population databases including gnomAD v2.1, v4.1, and gnomAD-Canada (>800,000 alleles screened).
SpliceAI in silico analysis predicts a potential splicing impact with a max delta score of 0.27 (DS_AL=0.27, DS_DL=0.26), exceeding the ATM VCEP 1.5.0 threshold of ≥0.2, consistent with the possible creation of an alternative splice acceptor or donor site.
The variant has not been reported in ClinVar and no functional studies (RNA splicing assays, ATM kinase activity, or radiosensitivity testing) have been published; thus no functional confirmation of the predicted splicing effect is available.
No A-T probands carrying this variant in trans with a pathogenic ATM variant have been reported, leaving the PM3 criterion unevaluable. Similarly, no cosegregation data (PP1) or case-control enrichment data (PS4) exist for this variant.
Applying the ATM VCEP 1.5.0 framework, two supporting-level pathogenic criteria are met: PM2_Supporting (absence from population databases) and PP3 (SpliceAI splicing prediction). No benign criteria are met. Under the ACMG/AMP 2015 combining rules adopted by the ATM VCEP, two supporting pathogenic criteria without any moderate, strong, or very strong criteria are insufficient to reach Likely Pathogenic. The variant is classified as a Variant of Uncertain Significance (VUS).
Resolution of this VUS would require: (1) RNA functional studies (RT-PCR or minigene assay) to confirm or exclude aberrant splicing, which could upgrade PVS1_Strength(RNA) or support BP7_RNA; (2) identification of the variant in trans with a pathogenic ATM variant in an A-T proband for PM3; and (3) reporting of this variant to ClinVar with clinical phenotype data.
No criteria match.
Met · 2
PM2 Supportingc.5178-28T>A is absent from all queried population databases: gnomAD v2.1 (exomes), gnomAD v4.1 (genomes+exomes), and gnomAD-Canada v1.0 (HostSeq genomes). Per the ATM VCEP 1.5.0, PM2_Supporting applies when the variant frequency is ≤0.001% in the gnomAD v4 dataset. Complete absence in >800,000 alleles satisfies this threshold. Details ▾Hide ▴
Evidence considered
- Absent from gnomAD v2.1 (0 alleles across all populations)
- Absent from gnomAD v4.1 (0 alleles across all populations)
- Absent from gnomAD-Canada v1.0
- ATM VCEP 1.5.0 PM2_Supporting threshold: frequency ≤0.001% in gnomAD v4
Sources
PP3 SupportingSpliceAI predicts a splicing impact for this intronic variant with a max delta score of 0.27 (DS_AL=0.27, DS_DL=0.26), exceeding the ATM VCEP 1.5.0 threshold of ≥0.2 for PP3. This criterion applies to intronic variants outside the donor and acceptor ±1,2 sites. The SpliceAI prediction suggests the variant may create an alternative splice acceptor or donor site. Per the VCEP, PP3 for splice predictions is applied at the Supporting strength level only. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta score = 0.27 (DS_AL=0.27
- DS_DL=0.26
- DS_AG=0.0
- DS_DG=0.01)
- Delta positions: acceptor loss at +28 bp
- donor loss at +169 bp
- suggesting potential cryptic splice site activation
- ATM VCEP 1.5.0 PP3 threshold: SpliceAI ≥0.2 for intronic variants outside canonicals ±1
- 2 sites
Still missing
- No RNA studies to confirm the predicted splicing impact
- SpliceAI delta of 0.27 is above the 0.2 threshold but below the 0.5 threshold often used for higher-confidence predictions
Sources
Not met · 6 · evaluated, threshold not reached
PVS1 c.5178-28T>A is an intronic variant located 28 bp upstream of the exon 35 acceptor splice site, outside the canonical ±1,2 splice dinucleotide. Per the ATM VCEP 1.5.0 PS1 splicing table, intronic variants outside the donor/acceptor ±1,2 dinucleotide use PP3 as the baseline computational code, not PVS1. PVS1 (predicted splice defect) is reserved for variants at donor/acceptor ±1,2 positions in the ATM VCEP framework. No RNA-level confirmation of aberrant splicing is available to support PVS1_Strength(RNA). Details ▾Hide ▴
Evidence considered
- SpliceAI max delta score = 0.27 (DS_AL=0.27
- DS_DL=0.26)
- indicating predicted splice impact
- Variant is at acceptor -28
- outside the ±1
- 2 canonical splice consensus
- ATM VCEP 1.5.0 PS1 table assigns PP3 (not PVS1) as baseline for variants outside ±1
- 2 dinucleotides
Still missing
- No RNA splicing studies (RT-PCR
- minigene assay) have been performed to confirm or exclude aberrant splicing
Sources
PS4 No case-control studies comparing the frequency of c.5178-28T>A in affected individuals versus controls have been performed. The ATM VCEP 1.5.0 requires a case-control study with p≤0.05 AND (odds ratio ≥2 OR lower 95% CI ≥1.5). The variant's extreme rarity (absent from gnomAD v2.1 and v4.1 with >800,000 alleles) precludes meaningful enrichment analysis without a very large disease-specific cohort. PS4_Moderate (proband counting) is explicitly not used per VCEP guidance. Details ▾Hide ▴
Evidence considered
- Variant is absent from gnomAD v2.1 and v4.1
- indicating extreme population rarity
- No published case-control study exists for this variant
- ATM VCEP 1.5.0: PS4_Moderate not used
- PS4_Strong requires case-control data
Still missing
- No case-control study in ATM-related cancer predisposition cohorts
- No A-T patient registry data with variant counts
- No BRIDGES or similar consortium data stratified by phenotype
Sources
BA1 c.5178-28T>A is absent from gnomAD v4.1 (0 alleles across all populations). The ATM VCEP 1.5.0 BA1 threshold requires a Grpmax Filtering AF >0.5% in the gnomAD v4 dataset. Complete absence fails this threshold by a wide margin. Details ▾Hide ▴
Evidence considered
- Absent from gnomAD v4.1 (0 alleles)
- ATM VCEP 1.5.0 BA1 threshold: Grpmax Filtering AF >0.5%
Sources
BS1 c.5178-28T>A is absent from gnomAD v4.1. The ATM VCEP 1.5.0 BS1 threshold requires a Grpmax Filtering AF >0.05% in the gnomAD v4 dataset. Complete absence fails this threshold. Details ▾Hide ▴
Evidence considered
- Absent from gnomAD v4.1 (0 alleles)
- ATM VCEP 1.5.0 BS1 threshold: Grpmax Filtering AF >0.05%
Sources
BP4 SpliceAI predicts a splicing impact for this variant with a max delta score of 0.27, which exceeds the ATM VCEP 1.5.0 BP4 threshold of ≤0.1 for 'no predicted impact via splicing.' The positive splice prediction precludes application of BP4. REVEL is not applicable as this is not a missense variant. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta = 0.27
- exceeding BP4 threshold of ≤0.1
- REVEL not applicable (intronic variant
- not missense)
- ATM VCEP 1.5.0 BP4: requires SpliceAI ≤0.1 for splicing
Sources
BP7 Although c.5178-28T>A is positioned at acceptor -28, which qualifies as 'deep intronic' (>21 bp from the acceptor site) per the ATM VCEP 1.5.0 BP7 definition, SpliceAI predicts a splicing impact with a max delta score of 0.27. BP7 is intended for deep intronic variants without predicted splice effects. The positive SpliceAI prediction argues against a benign interpretation via BP7. No RNA data are available to apply BP7_Strong(RNA) or BP7_Moderate(RNA) (observed lack of aberrant splicing). Details ▾Hide ▴
Evidence considered
- Variant position -28 qualifies as deep intronic (beyond -21 from acceptor)
- SpliceAI max delta 0.27 predicts splicing impact
- inconsistent with BP7 benign expectation
- No RNA data for BP7_RNA (lack of observed aberrant splicing)
Still missing
- No RNA studies confirming normal (non-aberrant) splicing
Sources
Not assessed · 7 · no assessment recorded
PS1 No known pathogenic or likely pathogenic ATM variant has been reported at the identical nucleotide position (c.5178-28) or within the same donor/acceptor motif with identical predicted splicing outcome. The ATM VCEP PS1 Splicing table requires a comparator reference variant classified as P/LP by VCEP specifications with matching predicted splice event. Without such a comparator, PS1 cannot be evaluated. Details ▾Hide ▴
Evidence considered
- The variant is absent from ClinVar
- so no P/LP comparator exists at this nucleotide
- ATM VCEP 1.5.0 PS1 Splicing table requires a reference variant at the same nucleotide or within the same donor/acceptor motif
Still missing
- Systematic search for pathogenic/likely pathogenic ATM variants at the same intronic position (c.5178-28) in locus-specific databases (LOVD
- ClinVar) returned no candidates
Sources
PS3 No variant-specific functional studies assessing ATM kinase activity, phosphorylation of ATM-specific targets (e.g., KAP1, p53), or radiosensitivity have been published for c.5178-28T>A. The ATM VCEP 1.5.0 requires functional assays that evaluate both an ATM-specific feature and radiosensitivity (PS3_Moderate) or an ATM-specific feature alone (PS3_Supporting). No such data exists for this deep intronic variant. Details ▾Hide ▴
Evidence considered
- PubMed and database searches (ClinVar
- LOVD) yielded no functional assay data for this exact variant
- No ATM-specific functional calibration set analogous to TP53 Giacomelli/Kato exists for ATM
Still missing
- No in vitro ATM kinase activity data
- No ATM substrate phosphorylation assays
- No radiosensitivity or ionizing radiation-induced foci formation assays
- No RNA splicing functional studies (which would inform PVS1_RNA rather than PS3 per VCEP guidance)
PM3 No observations of c.5178-28T>A occurring in trans with a known pathogenic or likely pathogenic ATM variant in an individual with Ataxia Telangiectasia (A-T) have been reported. The ATM VCEP 1.5.0 PM3/BP2 table assigns points per unrelated A-T proband based on zygosity and phenotype confidence (confirmed in trans: 2.0–4.0 points; phase unknown: 1.0–2.0 points). No proband data is available for this variant in ClinVar, LOVD, or the published literature. Details ▾Hide ▴
Evidence considered
- No A-T probands with this variant in trans with a P/LP ATM variant found in ClinVar or LOVD
- ATM VCEP 1.5.0 PM3 point system: requires ≥1 point (Supporting)
- ≥2 (Moderate)
- ≥4 (Strong)
- ≥8 (Very Strong)
Still missing
- No biallelic genotype data from diagnostic laboratories
- No A-T patient registry entries for this variant
- No newborn screening or carrier screening data
Sources
PP1 No family cosegregation data are available for c.5178-28T>A. The ATM VCEP 1.5.0 applies PP1 only to the autosomal recessive (A-T) condition, requiring affected relatives to carry both variants identified in the proband. For the autosomal dominant (cancer predisposition) condition, PP1 is explicitly not used because cosegregation analysis in low-penetrance genes can produce false positive results (PMID 32773770). No published pedigrees include this variant. Details ▾Hide ▴
Evidence considered
- No family data available in ClinVar
- LOVD
- or PubMed
- ATM VCEP 1.5.0: PP1 applies only to AR (A-T) condition
- not AD cancer predisposition
Still missing
- No pedigrees with this variant segregating with A-T
- No linkage data from research families
Sources
BS3 No well-established functional studies demonstrating that c.5178-28T>A has no damaging effect on ATM protein function or splicing have been published. The ATM VCEP 1.5.0 requires either rescue of both an ATM-specific feature (e.g., phosphorylation of ATM targets) AND radiosensitivity (BS3_Moderate), or rescue of either (BS3_Supporting). No functional data of any kind exists for this variant. Details ▾Hide ▴
Evidence considered
- No functional rescue assays published for this variant
- No minigene splicing assays showing normal splicing
Still missing
- No ATM kinase activity rescue data
- No radiosensitivity rescue data
- No RNA studies confirming normal splicing
BP2 No phased genotype data have been reported showing c.5178-28T>A occurring in cis (on the same allele) with a known pathogenic or likely pathogenic ATM variant in an unaffected individual ≥18 years old. The ATM VCEP 1.5.0 BP2 table assigns negative points based on zygosity and phenotype context (confirmed in trans in an unaffected individual: -4.0 points; homozygous in a database setting: -1.0 point). No such observations exist. Details ▾Hide ▴
Evidence considered
- No cis observations with a P/LP ATM variant in ClinVar
- LOVD
- or gnomAD
- Variant is too rare for statistical phasing in gnomAD
- ATM VCEP 1.5.0 BP2 point system: ≥ -1 point (Supporting)
- -2 (Moderate)
- ≤ -4 (Strong)
Still missing
- No phased haplotype data from any source
- No unaffected individuals with biallelic observations
Sources
PS5 PS5 is a placeholder for the ACMG/AMP 2015 framework. No evidence was identified or evaluated for this criterion. The variant type (intronic substitution) is not amenable to the typical applications of PS5. Details ▾Hide ▴
Evidence considered
- Not evaluated — no evidence targeted to this criterion
Still missing
- No evidence evaluated for PS5
Not applicable · 14· recorded as not applicable Show reasons ▾Hide reasons ▴
PS2 VCEPThe ATM VCEP 1.5.0 explicitly states PS2 is not applicable for autosomal dominant or autosomal recessive disease: '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.' Details ▾Hide ▴
PM1 VCEPThe ATM VCEP 1.5.0 explicitly states PM1 is not applicable: 'Do not use: Benign and pathogenic variants are known to occur within the same domains and germline mutational hotspots are not well defined at this time.' Details ▾Hide ▴
PM4 N/AThe ATM VCEP 1.5.0 restricts PM4 to stop-loss variants only: 'Do not use for in-frame insertions or deletions less than a single exon; Use for stop-loss variants, only.' c.5178-28T>A is a single-nucleotide intronic substitution, not a stop-loss variant. Details ▾Hide ▴
PM5 N/AThe ATM VCEP 1.5.0 restricts PM5_Supporting to frameshifting/truncating variants with premature termination codons upstream of p.Arg3047, or to splice variants where PVS1_VS(RNA) is applied based on high-quality observed splicing impact that is NMD-prone. This variant is an intronic substitution with no confirmed truncating effect and no RNA-level splicing data. The pm5_candidates.json confirms the PM5 mode is 'truncation_cutoff_gene_specific' with no eligible comparators. Details ▾Hide ▴
Evidence considered
- ATM VCEP 1.5.0 PM5_Supporting: requires truncating variants upstream of p.Arg3047 or PVS1_VS(RNA) with NMD-prone splicing defect
- No confirmed truncation effect and no RNA evidence for this variant
- pm5_candidates.json: recommendation level 'not_applicable' — truncation cutoff rule
- not classic missense PM5
Sources
cspec ↗pm5_candidates
PM6 VCEPThe ATM VCEP 1.5.0 explicitly states PM6 is not applicable for autosomal dominant or autosomal recessive disease: '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.' Details ▾Hide ▴
PP2 VCEPThe ATM VCEP 1.5.0 explicitly states PP2 is not applicable: 'Do not use: ATM does not have a defined low rate of missense benign variation.' Details ▾Hide ▴
PP4 VCEPThe ATM VCEP 1.5.0 explicitly states PP4 is not applicable. For the autosomal dominant condition, breast cancer has multiple genetic etiologies and no features distinguish hereditary from sporadic causes. For the autosomal recessive condition, such evidence is built into the PM3/BP2 table. Details ▾Hide ▴
PP5 VCEPThe ATM VCEP 1.5.0 explicitly states PP5 is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. Additionally, the variant is absent from ClinVar, so no reputable source has classified it as pathogenic. Details ▾Hide ▴
BS2 VCEPThe ATM VCEP 1.5.0 explicitly states BS2 is not applicable: 'Do not use: ATM has incomplete penetrance.' Details ▾Hide ▴
BS4 VCEPThe ATM VCEP 1.5.0 explicitly states BS4 is not applicable. For the autosomal dominant condition, cosegregation analysis in low-penetrance genes can lead to false positive results (PMID 32773770). For the autosomal recessive condition, informative instances of lack of cosegregation in A-T families are too rare to consider at this time. Details ▾Hide ▴
BP1 VCEPThe ATM VCEP 1.5.0 explicitly states BP1 is not applicable: 'Do not use: Missense pathogenic variants are known for ATM.' Details ▾Hide ▴
BP3 VCEPThe ATM VCEP 1.5.0 explicitly states BP3 is not applicable: 'Do not use.' This criterion concerns in-frame deletions/insertions in repetitive regions, which does not apply to this single-nucleotide intronic substitution. Details ▾Hide ▴
BP5 VCEPThe ATM VCEP 1.5.0 explicitly states BP5 is not applicable: '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.' Details ▾Hide ▴
BP6 VCEPThe ATM VCEP 1.5.0 explicitly states BP6 is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. Additionally, the variant is absent from ClinVar, so no external benign classification exists. Details ▾Hide ▴
Identifiers
- Gene
- ATM
- Transcript
- NM_000051.4
- Coding (HGVS c.)
- NM_000051.4:c.5178-28T>A
- Protein (HGVS p.)
- NP_000042.3:p.?
- GRCh38
- chr11:108301620 T>A
- GRCh37
- chr11:108172347 T>A
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
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Select a row to find it on the plot; use the link to open its page.
| Protein | Location | Classification | Link |
|---|
gnomAD v4.1
Allele count data not recorded
gnomAD v2.1
Allele count data not recorded
gnomAD-Canada v1.0
Allele count data not recorded
Statements
gnomAD v4.1
Absent from gnomAD v4.1.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI and Pangolin
Other predictors
- REVEL
- Not available
- BayesDel
- Not available
How the predictions were used
PP3 SupportingSpliceAI predicts a splicing impact for this intronic variant with a max delta score of 0.27 (DS_AL=0.27, DS_DL=0.26), exceeding the ATM VCEP 1.5.0 threshold of ≥0.2 for PP3. This criterion applies to intronic variants outside the donor and acceptor ±1,2 sites. The SpliceAI prediction suggests the variant may create an alternative splice acceptor or donor site. Per the VCEP, PP3 for splice predictions is applied at the Supporting strength level only. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta score = 0.27 (DS_AL=0.27
- DS_DL=0.26
- DS_AG=0.0
- DS_DG=0.01)
- Delta positions: acceptor loss at +28 bp
- donor loss at +169 bp
- suggesting potential cryptic splice site activation
- ATM VCEP 1.5.0 PP3 threshold: SpliceAI ≥0.2 for intronic variants outside canonicals ±1
- 2 sites
Still missing
- No RNA studies to confirm the predicted splicing impact
- SpliceAI delta of 0.27 is above the 0.2 threshold but below the 0.5 threshold often used for higher-confidence predictions
Sources
BP4 SpliceAI predicts a splicing impact for this variant with a max delta score of 0.27, which exceeds the ATM VCEP 1.5.0 BP4 threshold of ≤0.1 for 'no predicted impact via splicing.' The positive splice prediction precludes application of BP4. REVEL is not applicable as this is not a missense variant. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta = 0.27
- exceeding BP4 threshold of ≤0.1
- REVEL not applicable (intronic variant
- not missense)
- ATM VCEP 1.5.0 BP4: requires SpliceAI ≤0.1 for splicing
Sources
BP7 Although c.5178-28T>A is positioned at acceptor -28, which qualifies as 'deep intronic' (>21 bp from the acceptor site) per the ATM VCEP 1.5.0 BP7 definition, SpliceAI predicts a splicing impact with a max delta score of 0.27. BP7 is intended for deep intronic variants without predicted splice effects. The positive SpliceAI prediction argues against a benign interpretation via BP7. No RNA data are available to apply BP7_Strong(RNA) or BP7_Moderate(RNA) (observed lack of aberrant splicing). Details ▾Hide ▴
Evidence considered
- Variant position -28 qualifies as deep intronic (beyond -21 from acceptor)
- SpliceAI max delta 0.27 predicts splicing impact
- inconsistent with BP7 benign expectation
- No RNA data for BP7_RNA (lack of observed aberrant splicing)
Still missing
- No RNA studies confirming normal (non-aberrant) splicing
Sources
Statement
In silico
SpliceAI predicts possible splice impact for this variant (max delta score = 0.27).
0 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata.
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
gnomAD v4.1
Captured gnomAD v4.1 source record
Open source ↗
gnomAD v2.1
Captured gnomAD v2.1 source record
Open source ↗
SpliceAI Lookup
Recorded maximum delta 0.270
Open source ↗
ClinVar
Captured ClinVar source record
Open source ↗
COSMIC
Captured COSMIC source record
Open source ↗
ClinGen CSpec
Captured ClinGen CSpec source record
Open source ↗
All source links
- ClinGen CSpec ↗cspec.genome.network/cspec/ui/svi/doc/639508985
- ClinVar ↗www.ncbi.nlm.nih.gov/clinvar/?term=NM_000051.4%3Ac.5178-28T%3EA
- gnomAD v2.1 ↗gnomad.broadinstitute.org/variant/11-108172347-T-A?dataset=gnom…
- gnomAD v4.1 ↗gnomad.broadinstitute.org/variant/chr11-108301620-T-A?dataset=g…
- gnomAD-Canada ↗http://192.168.4.76:8001/variant/11-108301620-T-A
- SpliceAI Lookup ↗spliceailookup.broadinstitute.org/#variant=NM_000051.4%3Ac.5178…
- OncoKB ↗www.oncokb.org/gene/ATM/?
- COSMIC ↗cancer.sanger.ac.uk/cosmic/search?q=ATM+c.5178-28T%3EA
Statements for reports
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
gnomAD v4.1
Absent from gnomAD v4.1.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
ClinVar
This variant is absent from ClinVar.
In silico
SpliceAI predicts possible splice impact for this variant (max delta score = 0.27).
Somatic
This variant has not previously been reported in somatic cancers (COSMIC).