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ATM
Final classification
VUS
ATM c.5178-28T>A · p.?
ATM

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).

Gene
ATM
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.5178-28T>A
Consequence
N/A
GRCh38
chr11:108301620 T>A
GRCh37
chr11:108172347 T>A
Basis 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.
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.
Classification rationale
PM2PP3 VUS
ATM c.5178-28T>A

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).1 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.2 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.3 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).4 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.

PM2 + PP3 VUS
Gene diagram · NM_000051.4 · variants mapped to exon structure
ATM NM_000051.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 12 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
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.
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
PP3 supporting Pathogenic
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.
SpliceAI max delta score = 0.27 (DS_AL=0.27DS_DL=0.26DS_AG=0.0
Assessed · not applied
Pathogenic
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.
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.
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.
PS4 No case-control studies comparing the frequency of c.5178-28T>A in affected individuals versus controls have been performed.
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.
PP1 No family cosegregation data are available for c.5178-28T>A.
Benign
BA1 c.5178-28T>A is absent from gnomAD v4.1 (0 alleles across all populations).
BS1 c.5178-28T>A is absent from gnomAD v4.1.
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.
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.
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.
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.
N/A · 14 PS2 · PM1 · PM4 · PM5 · PM6 · PP2 · PP4 · PP5 · BS2 · BS4 · BP1 · BP3 · BP5 · BP6
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts possible splice impact for this variant (max delta score = 0.27).
Functional No data
No calibrated functional assay or RNA evidence was identified for this variant.
OncoKB ↗
COSMIC screenshot
COSMIC
Somatic evidence
COSMIC
This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant cancer hotspot.
COSMIC ↗
Sources & reference links
8Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC