Starting
Initialising…
0%
ATM
Final classification
VUS
ATM c.4397_4398delinsCG · p.Arg1466Pro
ATM

The ATM c.4397_4398delinsCG (p.Arg1466Pro) variant has been reported in ClinVar, where the overall expert-panel classification is uncertain significance and additional submissions range from uncertain significance to likely pathogenic and pathogenic.

Gene
ATM
Transcript
NM_000051.3
HGVS · transcript:coding
NM_000051.3:c.4397_4398delinsCG
Consequence
N/A
GRCh38
chr11:108289762 GA>CG
GRCh37
chr11:108160489 GA>CG
Basis Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework was evaluated deterministically with applied criteria: PS3 supporting, PM2 supporting; no rule matched the adjudicated criteria.
Richards et.al., 2015 - Combining rules v1.5.0 criteria-combination framework was evaluated deterministically with applied criteria: PS3 supporting, PM2 supporting; no rule matched the adjudicated criteria.
Classification rationale
PS3PM2 VUS
ATM c.4397_4398delinsCG

The ATM c.4397_4398delinsCG (p.Arg1466Pro) variant has been reported in ClinVar, where the overall expert-panel classification is uncertain significance and additional submissions range from uncertain significance to likely pathogenic and pathogenic.1 This variant is absent from gnomAD v4.1 and gnomAD v2.1, which is below the ATM VCEP PM2_supporting population threshold of less than or equal to 0.001%.2 In an ATM VCEP supplementary variant table, the equivalent single-nucleotide representation c.4397G>C (p.Arg1466Pro) is listed as non-functional with high confidence, supporting an abnormal ATM protein effect.3 SpliceAI predicts no significant splice impact for this variant with a max delta score of 0.01, and the equivalent c.4397G>C missense representation has a REVEL score of 0.677 in the ATM VCEP supplementary variant table, which is below the ATM PP3 threshold of greater than 0.7333 and above the BP4 threshold of less than or equal to 0.249.4

PS3 + PM2 VUS
3 vcep_suppl_tables1_pmid_40580951vcep_clingen_hbop_atm_supplementary_tables_1_and_2_v1cspec ↗
4 spliceai ↗vcep_suppl_tables1_pmid_40580951cspec ↗
Gene diagram · NM_000051.3 · variants mapped to exon structure
ATM NM_000051.3
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
      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 (4 clinical laboratories) and as Pathogenic (1 clinical laboratory) and as Likely pathogenic (1 clinical laboratory) and as Uncertain Significance 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 = 0.01).
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; curated oncogenicity label: Likely Oncogenic.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots