Starting
Initialising…
0%
ATM
Final classification
Pathogenic
ATM c.8315del · p.Gly2772GlufsTer34
ATM

The ATM c.8315del (p.Gly2772GlufsTer34) variant has been reported in ClinVar with pathogenic and likely pathogenic clinical submissions.

Gene
ATM
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.8315del
Consequence
N/A
GRCh38
chr11:108343266 AG>A
GRCh37
chr11:108213993 AG>A
Basis Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework: matched Rule4 (1 Pathogenic.Very Strong + Pathogenic.Supporting >=2) with applied criteria: PVS1 very strong, PM2 supporting, PM5 supporting; maps to Pathogenic.
Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework: matched Rule4 (1 Pathogenic.Very Strong + Pathogenic.Supporting >=2) with applied criteria: PVS1 very strong, PM2 supporting, PM5 supporting; maps to Pathogenic.
Classification rationale
PVS1PM2PM5 Pathogenic
ATM c.8315del

The ATM c.8315del (p.Gly2772GlufsTer34) variant has been reported in ClinVar with pathogenic and likely pathogenic clinical submissions.1 This variant is absent from gnomAD v4.1 and gnomAD v2.1, supporting rarity in the general population.2 ATM-specific criteria support pathogenic evidence for this truncating variant because p.(Gly2772GlufsTer34) introduces a premature termination codon upstream of the p.Arg3047 threshold used for ATM truncating variants, and ATM loss of function is an established disease mechanism.3 SpliceAI predicts no significant splice impact for this variant, with a maximum delta score of 0.14.4

PVS1 + PM2 + PM5 Pathogenic
3 cspec ↗pvs1_gene_contextpvs1_variant_assessmentvcep_a_t_m___p_v_s_1___1___5
Gene diagram · NM_000051.4 · variants mapped to exon structure
ATM NM_000051.4
Fetching transcript structure from UCSC…
Applied criteria · 3 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 · supports pathogenic
      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.
      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.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Pathogenic (2 clinical laboratories) and as Likely pathogenic (1 clinical laboratory).
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.14).
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB classifies this variant as Likely Oncogenic; biological effect: Likely Loss-of-function.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV53726306, n = 1 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots