Analysis in progress
Initialising…
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complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
EGFR
Final classification
VUS
EGFR c.2317_2318insCCCACCCCA · p.His773delinsProHisProAsn
EGFR

NM_005228.4:c.2317_2318insCCCACCCCA (p.His773delinsProHisProAsn) is an in-frame insertion in exon 20 of EGFR, within the tyrosine kinase domain.

Gene
EGFR
Transcript
NM_005228.4
HGVS · transcript:coding
NM_005228.4:c.2317_2318insCCCACCCCA
Consequence
N/A
GRCh38
chr7:55181326 C>CCCCACCCCA
GRCh37
chr7:55249019 C>CCCCACCCCA
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, PM4 moderate; combination = 1 moderate + 1 supporting, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, PM4 moderate; combination = 1 moderate + 1 supporting, which maps to VUS.
Classification rationale
PM2PM4 VUS
EGFR c.2317_2318insCCCACCCCA

NM_005228.4:c.2317_2318insCCCACCCCA (p.His773delinsProHisProAsn) is an in-frame insertion in exon 20 of EGFR, within the tyrosine kinase domain. This variant is absent from population databases including gnomAD v2.1, v4.1, and gnomAD-Canada (PM2_supporting).1 The in-frame insertion in a non-repeat functional domain meets PM4 at moderate strength. No variant-specific functional studies were identified in five reviewed publications; OncoKB classifies the variant as Likely Oncogenic in a somatic context, but this does not independently satisfy germline PS3.2 The variant is absent from ClinVar; no expert panel or submitter classification is available.3 The variant is not in a statistically significant mutational hotspot per Cancer Hotspots analysis, and in silico splicing predictors (SpliceAI max delta 0.08) do not indicate a splice effect.4 Overall, 1 moderate criterion (PM4) and 1 supporting criterion (PM2) are met. This does not reach the threshold for Likely Pathogenic (requires ≥2 moderate + ≥2 supporting, ≥3 moderate, or 1 strong + ≥1 moderate). The variant is classified as a Variant of Uncertain Significance (VUS) under generic ACMG/AMP 2015 criteria.5

PM2 + PM4 VUS
Gene diagram · NM_005228.4 · variants mapped to exon structure
EGFR NM_005228.4
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
      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
      Absent from gnomAD-Canada v1.0.
      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
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.08).
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-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
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 5 PMIDs not cited in assessment
      15897572 ↗ Mutation in the tyrosine kinase domain of epidermal growth factor receptor is a predictive and prognostic factor for gefitinib treatment in patients with non-small cell lung cancer. ONCOKB
      17686547 ↗ EGFR exon 20 insertion mutation in Japanese lung cancer. ONCOKB
      18676761 ↗ Lung cancer with epidermal growth factor receptor exon 20 mutations is associated with poor gefitinib treatment response. ONCOKB
      19536777 ↗ Second-line treatments after first-line gefitinib therapy in advanced nonsmall cell lung cancer. ONCOKB
      21764376 ↗ EGFR exon 20 insertion mutations in non-small-cell lung cancer: preclinical data and clinical implications. ONCOKB