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CCNE1
Final classification
VUS
CCNE1 c.254G>A · p.Arg85Gln
CCNE1

NM_001238.4:c.254G>A (p.Arg85Gln) is a missense variant in CCNE1.

Gene
CCNE1
Transcript
NM_001238.4
HGVS · transcript:coding
NM_001238.4:c.254G>A
Consequence
N/A
GRCh38
chr19:29817210 G>A
GRCh37
chr19:30308117 G>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 supporting, BP4 supporting; combination = 1 supporting + 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 supporting, BP4 supporting; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
CCNE1 c.254G>A

NM_001238.4:c.254G>A (p.Arg85Gln) is a missense variant in CCNE1. This variant is present at extremely low frequency in population databases: gnomAD v2.1 AF=0.0064% (16/251,482 alleles), gnomAD v4.1 AF=0.0040% (65/1,614,002 alleles), with no homozygotes observed. The maximum subpopulation frequency is 0.051% in the South Asian population. These frequencies meet the PM2 threshold (<0.1%).1 Multiple in silico prediction tools concordantly support a benign interpretation: REVEL score 0.031 (benign range), BayesDel score -0.586 (predicts benign), and SpliceAI max delta 0.00 (no predicted splicing impact). These findings meet the BP4 threshold (multiple lines of computational evidence suggest no impact).2 This variant has been reported in ClinVar as Uncertain significance by a single clinical laboratory (Ambry Genetics; criteria provided, single submitter). No expert panel review or pathogenic assertion is available.3 No variant-specific functional studies, de novo observations, segregation data, or case-control evidence are available. Applying the generic ACMG/AMP 2015 combination rules (PMID:25741868): PM2 (supporting) is balanced by BP4 (supporting). Neither a pathogenic combination (requiring ≥2 supporting or ≥1 moderate + ≥1 supporting) nor a benign/likely benign combination (requiring ≥2 supporting benign or ≥1 strong benign + ≥1 supporting benign) is satisfied.4 Overall classification: Uncertain significance.

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
4 generic_acmg_combination_rules
Gene diagram · NM_001238.4 · variants mapped to exon structure
CCNE1 NM_001238.4
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
      This variant is present in gnomAD v4.1 (AF= 4.02726e-05; MAF= 0.00403%, 65/1614002 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 0.000505095; MAF= 0.05051%, 46/91072 alleles, homozygotes = 0); grpmax FAF= 0.00038907.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 6.36228e-05; MAF= 0.00636%, 16/251482 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 0.000457277; MAF= 0.04573%, 14/30616 alleles, homozygotes = 0); grpmax FAF= 0.00027587.
      🇨🇦 CA
      This variant is present in gnomAD-Canada v1.0 (AF= 0.00010862480990658266, 2/18412 alleles, homozygotes = 0).
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.004% · 65 / 1,614,002
      0 hom · FAF 0.039%
      South Asian
      46 / 91,072
      0.051%
      Admixed American
      1 / 59,994
      0.0017%
      Remaining individuals
      1 / 62,480
      0.0016%
      European (non-Finnish)
      17 / 1,180,042
      0.0014%
      + 6 not observed (European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0064% · 16 / 251,482
      0 hom · FAF 0.028%
      South Asian
      14 / 30,616
      0.046%
      European (non-Finnish)
      2 / 113,758
      0.0018%
      + 6 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals)
      gnomAD Canada 🇨🇦
      0.011% · 2 / 18,412
      0 hom · FAF 0.026%
      South Asian
      2 / 1,362
      0.15%
      + 8 not observed (African/African American, Latino/Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Middle Eastern, European (non-Finnish), Remaining individuals)
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 3997617)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.031. BayesDel score = -0.586426.
      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. CCNE1, 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