Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
CCND1
Final classification
VUS
CCND1 c.517_519del · p.Glu173del
CCND1

NM_053056.3:c.517_519del (p.Glu173del) is an in-frame deletion of a single amino acid in exon 3 of CCND1. This variant is extremely rare in population databases (gnomAD v2.1: 1/250,946 alleles, AF = 0.00040%; gnomAD v4.1: 11/1,613,590 alleles, AF = 0.00068%), meeting PM2 at moderate strength.

Gene
CCND1
Transcript
NM_053056.3
HGVS · transcript:coding
NM_053056.3:c.517_519del
Consequence
N/A
GRCh38
chr11:69643929 CGGA>C
GRCh37
chr11:69458697 CGGA>C
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, PM4 moderate; combination = 2 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, PM4 moderate; combination = 2 moderate, which maps to VUS.
Classification rationale
PM2PM4 VUS
CCND1 c.517_519del

NM_053056.3:c.517_519del (p.Glu173del) is an in-frame deletion of a single amino acid in exon 3 of CCND1. This variant is extremely rare in population databases (gnomAD v2.1: 1/250,946 alleles, AF = 0.00040%; gnomAD v4.1: 11/1,613,590 alleles, AF = 0.00068%), meeting PM2 at moderate strength.1 As an in-frame deletion in a non-repeat region, the variant meets PM4 at moderate strength. The deletion removes Glu173, which lies within the cyclin C-terminal domain of CCND1.2 CCND1 has no established germline disease association and no CSPEC/VCEP framework exists for this gene. The pvs1_gene_context literature review claimed CCND1 loss-of-function as a germline mechanism, but the supporting papers do not actually study CCND1 germline disease: PMID:41429883 concerns PEG10/Silver-Russell syndrome, PMID:42295563 concerns DSP cardiomyopathy, PMID:30352907 concerns somatic urothelial carcinoma, PMID:30573562 concerns MYCN, and PMID:32737004 concerns colorectal cancer therapy. None of these papers discuss CCND1 germline loss-of-function variants.3 Two moderate pathogenic criteria are met (PM2, PM4), with zero benign criteria. Under generic ACMG/AMP 2015 combination rules, this is insufficient for a Likely Pathogenic classification (which requires at least 2 moderate + 1 supporting, or 1 pathogenic + ≥2 pathogenic criteria). The variant is classified as a Variant of Uncertain Significance (VUS).4

PM2 + PM4 VUS
2 pvs1_variant_assessment
3 pvs1_gene_context
4 generic_acmg_combination_rules
Gene diagram · NM_053056.3 · variants mapped to exon structure
CCND1 NM_053056.3
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= 6.8171e-06; MAF= 0.00068%, 11/1613590 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 1.09782e-05; MAF= 0.00110%, 1/91090 alleles, homozygotes = 0); grpmax FAF= 4.29e-06.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 3.98492e-06; MAF= 0.00040%, 1/250946 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.82068e-06; MAF= 0.00088%, 1/113370 alleles, homozygotes = 0).
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00068% · 11 / 1,613,590
      0 hom · FAF 0.00043%
      South Asian
      1 / 91,090
      0.0011%
      European (non-Finnish)
      10 / 1,180,006
      0.00085%
      + 8 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0004% · 1 / 250,946
      0 hom
      European (non-Finnish)
      1 / 113,370
      0.00088%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
      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).
      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. CCND1, a regulator of the cell cycle, is amplified in various cancer types including breast, head and neck, and bladder cancers.
      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