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CDKN2B
Final classification
VUS
CDKN2B c.338G>A · p.Gly113Asp
CDKN2B

NM_004936.3:c.338G>A (p.Gly113Asp) is a missense variant in exon 2 of CDKN2B, a tumor suppressor gene at 9p21.3 encoding the cyclin-dependent kinase inhibitor p15INK4b.

Gene
CDKN2B
Transcript
NM_004936.3
HGVS · transcript:coding
NM_004936.3:c.338G>A
Consequence
N/A
GRCh38
chr9:22006066 C>T
GRCh37
chr9:22006065 C>T
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 moderate, BP4 supporting benign; combination = 1 moderate + 1 supporting benign, 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 moderate, BP4 supporting benign; combination = 1 moderate + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
CDKN2B c.338G>A

NM_004936.3:c.338G>A (p.Gly113Asp) is a missense variant in exon 2 of CDKN2B, a tumor suppressor gene at 9p21.3 encoding the cyclin-dependent kinase inhibitor p15INK4b. This variant is extremely rare in large population databases: absent from gnomAD v2.1 and present at an allele frequency of 6.23×10⁻⁷ (1/1,606,290 alleles) in gnomAD v4.1, satisfying PM2 at moderate strength.1 Multiple lines of computational evidence suggest no significant impact on the gene product: BayesDel predicts a benign effect (−0.094), REVEL (0.484) falls below the commonly used pathogenic threshold of 0.5, and SpliceAI predicts no splicing alteration (max delta = 0.00), satisfying BP4 at supporting strength.2 This variant is absent from ClinVar with no submitter classifications, and has not been reported in the literature in association with disease.3 CDKN2B germline loss-of-function mutations have been associated with renal cell carcinoma (PMID:25873077), and 9p21.3 microdeletions encompassing CDKN2A/CDKN2B are associated with a cancer predisposition syndrome (PMID:35422439). However, the specific variant c.338G>A has not been reported in these or other published studies.4 No functional studies, case-control data, segregation data, or de novo reports are available for this variant. Per generic ACMG/AMP 2015 combination rules (PMID:25741868), a single moderate pathogenic criterion (PM2) and a single supporting benign criterion (BP4) do not meet the threshold for Likely Pathogenic or Likely Benign; the variant is classified as a Variant of Uncertain Significance (VUS).5

PM2 + BP4 VUS
2 bayesdelrevelspliceai ↗
4 pvs1_gene_context
5 generic_acmg_combination_rules
Gene diagram · NM_004936.3 · variants mapped to exon structure
CDKN2B NM_004936.3
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
      This variant is present in gnomAD v4.1 (AF= 6.22553e-07; MAF= 0.00006%, 1/1606290 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 1.60328e-05; MAF= 0.00160%, 1/62372 alleles, homozygotes = 0).
      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
      6.2e-05% · 1 / 1,606,290
      0 hom
      Remaining individuals
      1 / 62,372
      0.0016%
      + 9 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish))
      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 = 0.00). REVEL score = 0.484. BayesDel score = -0.0936784.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. CDKN2B, a tumor suppressor and cell cycle regulator, is inactivated by mutation or deletion in various cancer types.
      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
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots