Starting
Initialising…
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CCND2
Final classification
VUS
CCND2 c.389C>A · p.Ser130Tyr
CCND2

NM_001759.3:c.389C>A (p.Ser130Tyr) in CCND2 is absent from all population databases, meeting PM2 at moderate strength.

Gene
CCND2
Transcript
NM_001759.3
HGVS · transcript:coding
NM_001759.3:c.389C>A
Consequence
N/A
GRCh38
chr12:4276198 C>A
GRCh37
chr12:4385364 C>A
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; combination = 1 moderate, 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; combination = 1 moderate, which maps to VUS.
Classification rationale
PM2 VUS
CCND2 c.389C>A

NM_001759.3:c.389C>A (p.Ser130Tyr) in CCND2 is absent from all population databases, meeting PM2 at moderate strength.1 No other pathogenic or benign criteria were met. PVS1 is not applicable for this missense variant. All remaining criteria are either not met, not assessed due to absence of data, or not applicable to this variant type. With a single moderate pathogenic criterion (PM2) and no supporting criteria, the variant does not reach likely pathogenic, likely benign, or benign thresholds per generic ACMG/AMP 2015 combination rules (PMID:25741868). The variant is classified as a Variant of Uncertain Significance (VUS).2

PM2 VUS
2 generic_acmg_combination_rules
Gene diagram · NM_001759.3 · variants mapped to exon structure
CCND2 NM_001759.3
Fetching transcript structure from UCSC…
Applied criteria · 1 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 = 0.00). REVEL score = 0.585. BayesDel score = 0.118406.
      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. CCND2, a regulator of the cell cycle, is amplified 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
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots