Starting
Initialising…
0%
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 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      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