Starting
Initialising…
0%
ATM
Final classification
VUS
ATM c.8362C>T · p.His2788Tyr
ATM

The ATM c.8362C>T (p.His2788Tyr) variant has not been observed in somatic cancers in COSMIC and has been reported in ClinVar as uncertain significance by 2 clinical laboratories.

Gene
ATM
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.8362C>T
Consequence
N/A
GRCh38
chr11:108343315 C>T
GRCh37
chr11:108214042 C>T
Basis Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework was evaluated deterministically and no rule matched the adjudicated criteria.
Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework was evaluated deterministically and no rule matched the adjudicated criteria.
Classification rationale
PM2 VUS
ATM c.8362C>T

The ATM c.8362C>T (p.His2788Tyr) variant has not been observed in somatic cancers in COSMIC and has been reported in ClinVar as uncertain significance by 2 clinical laboratories.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, and the observed population frequency is therefore below the ATM PM2_Supporting threshold of <=0.001%.2 A multiplex functional study classified p.His2788Tyr as non-functional with high confidence, but the available data are based on olaparib fitness assays and do not yet establish the ATM-specific rescue framework required to apply ATM PS3 or BS3 without manual review.3 REVEL is 0.669, which is below the ATM PP3 threshold of >0.7333 and above the ATM BP4 missense threshold of <=0.249, while SpliceAI predicts no significant splice effect with a maximum delta score of 0.01, below the benign splicing threshold of <=0.1.4

PM2 VUS
3 PMID:40580951 ↗vcep_s_u_p_p_l___t_a_b_l_e_s_1___p_m_i_d___4_0_5_8_0_9_5_1cspec ↗
Gene diagram · NM_000051.4 · variants mapped to exon structure
ATM NM_000051.4
Fetching transcript structure from UCSC…
Applied criteria · 1 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.
      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 Uncertain significance (2 clinical laboratories).
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01).
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB has not reviewed this specific variant; no variant-level oncogenicity or biological effect is available. Gene-level context: ATM, a kinase involved in the DNA damage response, is mutated in various solid and hematologic malignancies.
      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