Starting
Initialising…
0%
ATM
Final classification
Likely Pathogenic
ATM c.8395_8404del · p.Phe2799LysfsTer4
ATM

ATM HBOP VCEP v1.5 supports PVS1 for null variants through the ATM PVS1 decision tree, and this variant is an exonic frameshift with predicted consequence p.(Phe2799LysfsTer4)/p.(F2799Kfs*4).

Gene
ATM
Transcript
NM_000051.4
HGVS · transcript:coding
NM_000051.4:c.8395_8404del
Consequence
N/A
GRCh38
chr11:108343337 ATTTCAGTGCC>A
GRCh37
chr11:108214064 ATTTCAGTGCC>A
Basis ATM HBOP VCEP v1.5 ACMG/AMP specification; applied evidence PVS1_VeryStrong + PM5_Supporting (Bayesian point total verified from applied evidence = 9).
ATM HBOP VCEP v1.5 ACMG/AMP specification; applied evidence PVS1_VeryStrong + PM5_Supporting (Bayesian point total verified from applied evidence = 9).
Classification rationale
PVS1PM5 Likely Pathogenic
ATM c.8395_8404del

ATM HBOP VCEP v1.5 supports PVS1 for null variants through the ATM PVS1 decision tree, and this variant is an exonic frameshift with predicted consequence p.(Phe2799LysfsTer4)/p.(F2799Kfs*4).1 ATM-specific PM5_Supporting applies to truncating variants with premature termination codons upstream of p.Arg3047; this variant truncates at codon 2802, upstream of that boundary.2 PM2 was not applied because gnomAD v4 shows 20/1613922 alleles (0.00124%), slightly above the ATM PM2_Supporting threshold of 0.001%.3 ClinVar contains a concordant ClinGen HBOP expert-panel Pathogenic classification for this variant, but that assertion was treated as contextual support rather than as a standalone ACMG criterion.4

PVS1 + PM5 Likely Pathogenic
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
      Allele frequency by ancestry
      three datasets · side by side
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Pathogenic (23 clinical laboratories) and as Likely pathogenic (1 clinical laboratory) and as Pathogenic by ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Variant Curation Expert Panel, ClinGen (expert panel).
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07).
      Functional / OncoKB screenshot
      Functional
      OncoKB classifies this variant as Likely Oncogenic; biological effect: Likely Loss-of-function.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence
      COSMIC
      This variant has previously been reported in somatic cancers (COSMIC; COSV53730617, n = 6 times).
      Hotspots
      This variant does not lie in a statistically significant cancer hotspot.
      Sources & reference links
      6Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB