Starting
Initialising…
0%
ATM
Final classification
Pathogenic
ATM c.4300A>T · p.Lys1434Ter
ATM

The ATM c.4300A>T (p.Lys1434Ter; p.K1434*) variant has not been observed in somatic cancers in COSMIC and has not been reported in ClinVar.

Gene
ATM
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.4300A>T
Consequence
N/A
GRCh38
chr11:108289665 A>T
GRCh37
chr11:108160392 A>T
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: PM5 supporting, PM2 supporting, PVS1 very strong; 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: PM5 supporting, PM2 supporting, PVS1 very strong; maps to Pathogenic.
Classification rationale
PM5PM2PVS1 Pathogenic
ATM c.4300A>T

The ATM c.4300A>T (p.Lys1434Ter; p.K1434*) variant has not been observed in somatic cancers in COSMIC and has not been reported in ClinVar.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, placing it below the ATM VCEP PM2_Supporting threshold of 0.001% and well below the BS1 (>0.05%) and BA1 (>0.5%) thresholds.2 This is a nonsense variant predicted to introduce a premature stop codon at Lys1434; SpliceAI predicts no significant splice impact with a maximum delta score of 0.03, supporting interpretation as a truncating loss-of-function event rather than a splice-altering event.3

PM5 + PM2 + PVS1 Pathogenic
3 spliceai ↗pvs1_variant_assessmentvcep_atm_pvs1_1_5cspec ↗
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 is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). BayesDel score = 0.634849.
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      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