Starting
Initialising…
0%
ATM
Final classification
Likely Pathogenic
ATM c.9041_9042del · p.Gln3014ArgfsTer48
ATM

PVS1 is met at Very Strong strength: NM_000051.4:c.9041_9042del is a frameshift deletion resulting in a premature termination codon (p.Gln3014ArgfsTer48) upstream of the p.Arg3047 threshold in a gene where loss of function is an established disease mechanism. The PTC is NMD-competent per the ClinGen SVI PVS1 framework and the ATM VCEP PVS1 decision tree.

Gene
ATM
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.9041_9042del
Consequence
N/A
GRCh38
chr11:108365377 CAA>C
GRCh37
chr11:108236104 CAA>C
Basis Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework: matched Rule19 (1 Pathogenic.Very Strong + 1 Pathogenic.Supporting) with applied criteria: PVS1 very strong, PM2 supporting; maps to Likely Pathogenic.
Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework: matched Rule19 (1 Pathogenic.Very Strong + 1 Pathogenic.Supporting) with applied criteria: PVS1 very strong, PM2 supporting; maps to Likely Pathogenic.
Classification rationale
PVS1PM2 Likely Pathogenic
ATM c.9041_9042del

PVS1 is met at Very Strong strength: NM_000051.4:c.9041_9042del is a frameshift deletion resulting in a premature termination codon (p.Gln3014ArgfsTer48) upstream of the p.Arg3047 threshold in a gene where loss of function is an established disease mechanism. The PTC is NMD-competent per the ClinGen SVI PVS1 framework and the ATM VCEP PVS1 decision tree.1 PM2 is met at Supporting strength: this variant is absent from gnomAD v4.1 (allele count 0), meeting the ATM VCEP threshold of ≤0.001% allele frequency in gnomAD v4.2 No benign or conflicting evidence was identified: BA1 and BS1 are not met (variant absent from gnomAD); PS3/BS3 functional evidence was sought but no variant-specific functional data were found in the reviewed literature or VCEP reference tables.3 Under the ATM VCEP v1.5.0 final combination rules, Rule 19 is triggered: 1 Very Strong pathogenic criterion (PVS1) + 1 Supporting pathogenic criterion (PM2_Supporting) yields a classification of Likely Pathogenic.4

PVS1 + PM2 Likely Pathogenic
4 cspec ↗final_classification_framework
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 · 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.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      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 No data
      No in-silico prediction was recorded for this variant.
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
      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 not previously been reported in somatic cancers (COSMIC).
      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
      Triaged references · 3 PMIDs not cited in assessment
      27413114 ↗ ATM Mutations in Cancer: Therapeutic Implications. ONCOKB
      30348496 ↗ Inactive Atm abrogates DSB repair in mouse cerebellum more than does Atm loss, without causing a neurological phenotype. ONCOKB
      30553448 ↗ Loss of ATM positively regulates Rac1 activity and cellular migration through oxidative stress. ONCOKB