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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 applied · 16 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 moderate Pathogenic
Variant is absent from all population databases: gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 (allele count 0 across all datasets). Meets PM2 threshold of <0.1% for non-VCEP generic ACMG.
gnomAD v2.1: absentgnomAD v4.1: absentgnomAD-Canada: AC=0
Assessed · not applied
Pathogenic
PS2 No de novo data (with confirmed paternity and maternity) are available for this variant in ClinVar or the literature.
PS3 No variant-specific functional studies identified.
PS4 No case-control or cohort data available.
PM1 Residue Ser130 is not located in a statistically significant mutational hotspot (Cancer Hotspots: not significant).
PM6 No de novo observation data available for this variant in ClinVar or literature; PM6 cannot be assessed without a de novo report.
PP1 No co-segregation data available.
PP2 CCND2 is associated with MPPH syndrome where heterozygous missense variants are a known disease mechanism (GeneReviews, PMID:27854409).
PP3 Conflicting in silico predictions: REVEL score 0.585 (borderline, just above 0.5 threshold), BayesDel score 0.118 (low, not supporting pathogenicity), SpliceAI max delta 0.00 (no splice effect).
PP4 No patient phenotype or clinical data are available; variant is not reported in ClinVar with associated phenotype information.
Benign
BA1 Variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (AF=0).
BS1 Variant is absent from all population databases (AF=0).
BS3 No functional studies assessing this variant are available.
BS4 No family segregation data available; no reports of non-segregation with disease phenotype.
BP2 No phase data available.
BP4 In silico predictions do not support a benign interpretation.
BP5 No data available regarding an alternate molecular basis for disease in any individual carrying this variant.
N/A · 11 PVS1 · PS1 · PM3 · PM4 · PM5 · PP5 · BS2 · BP1 · BP3 · BP6 · BP7
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