Starting
Initialising…
0%
NFE2L2
Final classification
VUS
NFE2L2 c.100C>G · p.Arg34Gly
NFE2L2

NM_006164.4:c.100C>G (p.Arg34Gly) is a missense variant in exon 2 of NFE2L2. It is absent from gnomAD v2.1 and v4.1 population databases (PM2_Supporting).

Gene
NFE2L2
Transcript
NM_006164.4
HGVS · transcript:coding
NM_006164.4:c.100C>G
Consequence
N/A
GRCh38
chr2:177234217 G>C
GRCh37
chr2:178098945 G>C
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: PM1 moderate, PM2 supporting; 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: PM1 moderate, PM2 supporting; combination = 1 moderate + 1 supporting, which maps to VUS.
Classification rationale
PM1PM2 VUS
NFE2L2 c.100C>G

NM_006164.4:c.100C>G (p.Arg34Gly) is a missense variant in exon 2 of NFE2L2. It is absent from gnomAD v2.1 and v4.1 population databases (PM2_Supporting).1 The variant is located at codon 34 within the Neh2 domain (residues 16–89), the KEAP1-binding degron that is a critical and well-established functional domain. Arg34 is a statistically significant cancer hotspot residue, and other missense alterations at this codon (R34Q, R34P) are recurrently observed in NSCLC and other cancers with no benign variation at this codon (PM1).2 The variant has been reported in COSMIC (COSV67960061, n=42) as a somatic mutation. OncoKB classifies it as Likely Oncogenic (somatic context). These somatic observations do not directly inform germline pathogenicity under ACMG/AMP.3 In silico predictions are equivocal: REVEL score 0.543 (borderline), BayesDel score 0.170 (low), and SpliceAI max delta 0.00. These do not meet the threshold for PP3 or BP4.4 No functional studies, case-control data, de novo observations, segregation data, or authoritative germline classifications are available for this variant. The majority of criteria cannot be assessed. Applying the generic ACMG/AMP 2015 combination rules: PM1 (moderate) + PM2_Supporting (supporting) = 1 moderate + 1 supporting. This is insufficient for a Likely Pathogenic classification (requires 2 moderate, or 1 strong + 1 moderate, or 1 strong + ≥2 supporting). No benign criteria are met. The variant is classified as a Variant of Uncertain Significance (VUS).5

PM1 + PM2 VUS
Gene diagram · NM_006164.4 · variants mapped to exon structure
NFE2L2 NM_006164.4
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
      This variant is absent from gnomAD-Canada.
      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 has been reported in ClinVar but submission details could not be extracted. (ClinVarID = 3258027)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.543. BayesDel score = 0.170416.
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Hotspot
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV67960061, n = 42 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Literature · how each cited paper was used
      1papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 6 further PMIDs triaged but not cited — see Sources & References.
      Genomic structure and variation of nuclear factor (erythroid-derived 2)-like 2.
      Found
      Other missense variants at codon 34 (R34Q/c.101G>A R34P/c.101G>C) are reported as somatic mutations in NSCLC and other cancers in PMID:23936606.
      Applied to
      PM1 supports · met
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 6 PMIDs not cited in assessment
      30150714 ↗ A catalogue of somatic NRF2 gain-of-function mutations in cancer. ONCOKB
      21897267 ↗ Association of keap1 and nrf2 genetic mutations and polymorphisms with endometrioid endometrial adenocarcinoma survival. ONCOKB
      35101336 ↗ Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC). CLINVAR
      22918138 ↗ Opportunities and challenges associated with clinical diagnostic genome sequencing: a report of the Association for Molecular Pathology. CLINVAR
      34131312 ↗ Chromosomal microarray analysis, including constitutional and neoplastic disease applications, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). CLINVAR
      23619274 ↗ American College of Medical Genetics and Genomics technical standards and guidelines: microarray analysis for chromosome abnormalities in neoplastic disorders. CLINVAR