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CCNE1
Final classification
VUS
PM2BP4
CCNE1
c.617A>G
p.Tyr206Cys
missense · exon 8

CCNE1 encodes cyclin E1, a regulatory protein that partners with cyclin-dependent kinase 2 (CDK2) to control the G1/S transition of the cell cycle, the checkpoint where cells commit to division. Cyclin E1-CDK2 inactivates the retinoblastoma protein and triggers the gene expression program needed to enter S phase. CCNE1 is an oncogene: its amplification and overexpression are found in many cancers, including breast and ovarian cancer, where they contribute to chromosome instability and are often linked to poorer outcomes.

This variant

CCNE1 promotes cancer chiefly through amplification and overexpression, not established inherited missense mechanisms. This variant is a VUS: it is rare in population databases and predicted not to affect splicing, but no functional or clinical evidence yet shows whether p.Tyr206Cys alters cyclin E1-CDK2 activity.

Transcript
NM_001238.4
HGVS · transcript:coding
NM_001238.4:c.617A>G
GRCh38
chr19:29821729 A>G
GRCh37
chr19:30312636 A>G
Basis Generic ACMG/AMP 2015 rules applied (no CCNE1-specific framework exists): only PM2 and BP4, both supporting strength, were met — insufficient to classify beyond VUS.
Generic ACMG/AMP 2015 rules applied (no CCNE1-specific framework exists): only PM2 and BP4, both supporting strength, were met — insufficient to classify beyond VUS.
Classification rationale
PM2 BP4 VUS
CCNE1 c.617A>G missense · exon 8

PM2 (Supporting): rare in gnomAD — highest observed allele frequency 0.05612%, below the 0.1% rarity threshold. BP4 (Supporting): SpliceAI max delta 0.011, far below the ~0.2 splice-altering cutoff, indicating no splice impact. Synthesis: two supporting criteria do not reach the strength required for a pathogenic or benign call under generic ACMG/AMP 2015 combination rules, so the variant is classified as VUS.

PM2 + BP4 VUS
Gene diagram · NM_001238.4 · variants mapped to exon structure
CCNE1 NM_001238.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 22 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
Met (supporting): highest observed allele frequency is 0.05612% (gnomAD v2.1 African/African American), below the 0.1% rarity threshold.
gnomAD v2.1: 62/282,496 alleles (AF 0.02195%), highest African/African American AF 0.05612%, zero homozygotes.gnomAD v4.1: 496/1,602,884 alleles (AF 0.03094%), highest African/African American AF 0.04547%, grpmax FAF 0.034706%, zero homozygotes.gnomAD-Canada v1.0: 2/18,422 alleles (AF 0.01086%), zero homozygotes.
BP4 supporting Benign
Met (supporting): SpliceAI max delta 0.011, far below the ~0.2 splice-altering cutoff, indicating no splice impact.
SpliceAI max delta score = 0.011 (all four component scores DS_AG/DS_AL/DS_DG/DS_DL <= 0.011), interpreted against the ~0.2 high-recall splice-altering threshold from Jaganathan K et al., Cell 2019, PMID 30661751, indicating no predicted splicing impact.REVEL score 0.465 (local REVEL v1.3 lookup) does not cross the ClinGen SVI-calibrated BP4-supporting threshold (<=0.290) from Pejaver V et al., PMID 36413997, so it is indeterminate and not independently used to support BP4.BayesDel score 0.115237 reported in evidence.json/prefetch.json but excluded because no verified published calibration threshold for BayesDel is available to this pipeline.
Assessed · not applied · 5 not met · 17 not assessed
Pathogenic
PS1 Not assessed: no alternate nucleotide change producing p.Tyr206Cys with an established pathogenic classification was found.
PS2 Not assessed: no de novo observation, parental genotypes, or phenotype data were available.
PS3 Not assessed: no functional assay data (e.g., cyclin E1-CDK2 activity) for p.Tyr206Cys were identified in any source.
PS4 Not assessed: no case-control or cohort enrichment data for this variant were available.
PM1 Not met: residue 206 is not a significant hotspot per Cancerhotspots.org, and no evidence places it in a critical functional domain.
PM3 Not assessed: no affected proband with this variant in trans with a pathogenic allele, or phase/segregation data, was documented.
PM5 Not assessed: no alternate missense change at codon 206 with an established pathogenic classification was found.
PM6 Not assessed: no de novo observation with confirmed parentage was documented.
PP1 Not assessed: no pedigree, relative genotypes, or informative meioses were provided.
PP2 Not assessed: no gene-specific evidence that missense variants cause disease; CCNE1 acts mainly through amplification and gain of function.
PP3 Not met: REVEL score 0.465 lies in the indeterminate zone between the 0.290 benign and 0.644 pathogenic thresholds.
PP4 Not assessed: no proband phenotype or phenotype-to-gene specificity evidence was available.
PP5 Not assessed: the exact variant is absent from ClinVar, so no expert-panel pathogenic assertion exists.
Benign
BA1 Not met: highest population allele frequency is 0.05612%, far below the 5% BA1 threshold.
BS1 Not met: highest ancestry-group allele frequency is 0.05612%, below the 0.3% BS1 threshold.
BS2 Not met: gnomAD v2.1 and v4.1 report zero homozygotes and no qualifying healthy-adult carrier data.
BS3 Not assessed: no functional assay data showing normal activity for p.Tyr206Cys were identified.
BS4 Not assessed: no non-segregation observation (affected non-carrier or unaffected carrier) was provided.
BP1 Not assessed: no gene-level mechanism data indicating CCNE1 disease is predominantly loss-of-function.
BP2 Not assessed: no observation of this variant in cis with a pathogenic allele or an alternative molecular diagnosis.
BP5 Not assessed: no affected individual or independent molecular diagnosis was provided to establish an alternative cause.
BP6 Not assessed: the exact variant is absent from ClinVar, so no expert-panel benign assertion exists.
N/A · 4 PVS1 · PM4 · BP3 · BP7
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= 0.000309442; MAF= 0.03094%, 496/1602884 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000454704; MAF= 0.04547%, 34/74774 alleles, homozygotes = 0); grpmax FAF= 0.00034706.
v2.1
This variant is present in gnomAD v2.1 (AF= 0.000219472; MAF= 0.02195%, 62/282496 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000561212; MAF= 0.05612%, 14/24946 alleles, homozygotes = 0); grpmax FAF= 0.00037677.
🇨🇦 CA
This variant is present in gnomAD-Canada v1.0 (AF= 0.00010856584518510477, 2/18422 alleles, homozygotes = 0).
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.031% · 496 / 1,602,884
0 hom · FAF 0.035%
African/African American
34 / 74,774
0.045%
European (non-Finnish)
440 / 1,169,980
0.038%
Remaining individuals
14 / 62,100
0.023%
East Asian
3 / 44,822
0.0067%
European (Finnish)
3 / 64,004
0.0047%
South Asian
2 / 90,782
0.0022%
+ 4 not observed (Admixed American, Amish, Middle Eastern, Ashkenazi Jewish)
gnomAD v2.1
0.022% · 62 / 282,496
0 hom · FAF 0.038%
African/African American
14 / 24,946
0.056%
European (non-Finnish)
41 / 129,010
0.032%
Remaining individuals
2 / 7,212
0.028%
South Asian
2 / 30,572
0.0065%
East Asian
1 / 19,936
0.005%
European (Finnish)
1 / 25,108
0.004%
Admixed American
1 / 35,346
0.0028%
+ 1 not observed (Ashkenazi Jewish)
gnomAD Canada 🇨🇦
0.011% · 2 / 18,422
0 hom · FAF 0.003%
European (non-Finnish)
2 / 11,742
0.017%
+ 8 not observed (African/African American, Latino/Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Middle Eastern, Remaining individuals, South Asian)
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 = 0.01). REVEL score = 0.465. BayesDel score = 0.115237.
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 previously been reported in somatic cancers (COSMIC; COSV105008511, n = 2 times).
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