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Variant interpretation report

CCND1 c.723G>A, p.(Pro241=)

NM_053056.3:c.723G>A NP_444284.1:p.(Pro241=) View identifiers
Classification
Benign

Variant description:

No variant summary was recorded for this case.

Five-step scale from benign to pathogenic. This variant is benign. Select a step to read what it means.

Benign.A benign classification under the recorded framework.

In plain language

Gene-level background from the recorded interpretation.

About CCND1

No gene-level summary was recorded for this case.

LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
01The reasoning

How it was classified

The recorded framework is Not recorded. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.

Recorded applied criteria

The applied criteria and their strengths are shown as assessed under the stated framework.

Pathogenic evidence criteria: 0 Benign evidence criteria: 6
Pathogenic criteria applied · 0

No pathogenic criterion marked as applied in the recorded assessment.

Benign criteria applied · 6
BA1Stand alone
BA1 · stand alone

Allele frequency far exceeds the 1% BA1 threshold: 44.66% in gnomAD v2.1 (125,943/282,012 alleles, 29,329 homozygotes) and 44.40% in gnomAD v4.1 (716,284/1,613,168 alleles, 162,210 homozygotes). This is a common polymorphism present in all populations, with highest frequency in East Asians (56.69% in v2.1).

BS1Strong
BS1 · strong

Allele frequency exceeds the 0.3% BS1 threshold. Superseded by BA1 for classification purposes but independently meets BS1 criteria.

BS2Strong
BS2 · strong

Observed in 29,329 homozygous individuals in gnomAD v2.1 and 162,210 homozygous individuals in gnomAD v4.1. This high number of healthy adult homozygotes demonstrates compatibility with normal development and excludes pathogenicity for any early-onset, fully penetrant Mendelian disorder.

BP4Supporting
BP4 · supporting

Multiple lines of computational evidence suggest no impact on the gene product. SpliceAI max delta = 0.02 predicts no splicing effect. The variant is synonymous (p.Pro241=) and does not alter the amino acid sequence. REVEL and BayesDel scores are unavailable, as expected for a synonymous variant with no amino acid change.

BP6Supporting
BP6 · supporting

ClinVar reports this variant as Benign (Variation ID 13755) with review status 'criteria provided, single submitter,' from 2 clinical laboratories. A reputable source classifies this variant as benign.

BP7Supporting
BP7 · supporting

Synonymous variant (p.Pro241=) at a nucleotide position where SpliceAI predicts no splicing impact (max delta = 0.02). The variant does not alter the amino acid sequence and is not predicted to affect splicing, meeting BP7 criteria.

Recorded classification: Benign

gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: BA1 stand-alone benign, BS1 strong benign, BS2 strong benign, BP4 supporting benign, BP6 supporting benign, BP7 supporting benign; combination = 1 stand-alone benign + 2 strong benign + 3 supporting benign, which maps to Benign.

02The sources

Evidence at a glance

Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.

gnomAD v4.1
gnomAD v2.1
Population frequency
716,284 / 1,613,168 alleles

gnomAD v4.1: 716,284 / 1,613,168 alleles. Recorded AF 0.444023. Recorded homozygote count 162210.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 0.446587; MAF= 44.65874%, 125943/282012 alleles, homozygotes = 29329) and has highest observed frequency in the East Asian population (AF= 0.566911; MAF= 56.69110%, 11294/19922 alleles, homozygotes = 3160); grpmax FAF= 0.559639.

gnomAD-Canada

This variant is present in gnomAD-Canada v1.0 (AF= 0.4660823170731707, 8561/18368 alleles, homozygotes = 2065).

SpliceAI score
0.020 maximum delta

Recorded SpliceAI maximum delta score: 0.020. Refer to the recorded PP3/BP4 rationale for interpretation.

ClinVar submissions
2 reported laboratory submissions

2 Benign. ClinVar API review status: criteria provided, multiple submitters, no conflicts.

Functional evidence
Statement recorded

OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.

No listed criterion applied OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
79 recorded samples

This variant has previously been reported in somatic cancers (COSMIC; COSV57118864, n = 79 times).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.

For specialists

Technical detail

ACMG/AMP criteria under Not recorded, with the data and sources behind each one.

26 criteria with recorded statuses: 6 met · 7 not met · 8 not assessed · 5 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.

Met Not met Not assessed Not applicable

NM_053056.3:c.723G>A (p.Pro241=) is a synonymous variant in CCND1 with an allele frequency of 44.66% in gnomAD v2.1 (125,943/282,012 alleles, 29,329 homozygotes) and 44.40% in gnomAD v4.1, meeting BA1 (stand-alone benign).

The variant has been observed in 29,329 homozygous individuals in gnomAD v2.1, demonstrating compatibility with normal health and meeting BS2.

ClinVar classifies this variant as Benign (Variation ID 13755, 2 clinical laboratories), meeting BP6.

SpliceAI predicts no splicing impact (max delta = 0.02) and the variant is synonymous (p.Pro241=), meeting BP7 and BP4.

No publications identified in the case materials mention NM_053056.3:c.723G>A specifically; papers cited by ClinVar submissions discuss the CCND1 c.870G>A polymorphism which is a different variant.

Met · 6

BA1 Stand aloneAllele frequency far exceeds the 1% BA1 threshold: 44.66% in gnomAD v2.1 (125,943/282,012 alleles, 29,329 homozygotes) and 44.40% in gnomAD v4.1 (716,284/1,613,168 alleles, 162,210 homozygotes). This is a common polymorphism present in all populations, with highest frequency in East Asians (56.69% in v2.1). Details ▾Hide ▴
Evidence considered
  • gnomAD v2.1 AF=44.66% (125
  • 943/282
  • 012 alleles
  • 29
  • 329 homozygotes)
  • gnomAD v4.1 AF=44.40% (716
  • 284/1
  • 613
  • 168 alleles
  • 162
  • 210 homozygotes)
  • common polymorphism across all populations.
Sources
BS1 StrongAllele frequency exceeds the 0.3% BS1 threshold. Superseded by BA1 for classification purposes but independently meets BS1 criteria. Details ▾Hide ▴
Evidence considered
  • gnomAD AF = 44.66% (v2.1)
  • 44.40% (v4.1)
  • well above BS1 threshold of >0.3%.
Sources
BS2 StrongObserved in 29,329 homozygous individuals in gnomAD v2.1 and 162,210 homozygous individuals in gnomAD v4.1. This high number of healthy adult homozygotes demonstrates compatibility with normal development and excludes pathogenicity for any early-onset, fully penetrant Mendelian disorder. Details ▾Hide ▴
Evidence considered
  • 29
  • 329 homozygotes in gnomAD v2.1
  • 162
  • 210 homozygotes in gnomAD v4.1
  • variant is compatible with normal health in the homozygous state.
Sources
BP4 SupportingMultiple lines of computational evidence suggest no impact on the gene product. SpliceAI max delta = 0.02 predicts no splicing effect. The variant is synonymous (p.Pro241=) and does not alter the amino acid sequence. REVEL and BayesDel scores are unavailable, as expected for a synonymous variant with no amino acid change. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta score = 0.02 (no predicted splicing impact)
  • synonymous variant (p.Pro241=) with no amino acid change.
Sources
BP6 SupportingClinVar reports this variant as Benign (Variation ID 13755) with review status 'criteria provided, single submitter,' from 2 clinical laboratories. A reputable source classifies this variant as benign. Details ▾Hide ▴
Evidence considered
  • ClinVar: Benign classification (Variation ID 13755)
  • 2 clinical laboratories
  • review status: criteria provided
  • single submitter.
Sources
BP7 SupportingSynonymous variant (p.Pro241=) at a nucleotide position where SpliceAI predicts no splicing impact (max delta = 0.02). The variant does not alter the amino acid sequence and is not predicted to affect splicing, meeting BP7 criteria. Details ▾Hide ▴
Evidence considered
  • Synonymous substitution p.Pro241= with no amino acid change
  • SpliceAI max delta = 0.02 (no splicing impact predicted).
Sources

Not met · 7 · evaluated, threshold not reached

PS3 No functional studies of NM_053056.3:c.723G>A or a systematically characterized range that includes this position were identified in the literature. The variant is synonymous and produces no amino acid change. Details ▾Hide ▴
Evidence considered
  • No variant-specific functional data identified
  • synonymous variant with no predicted protein alteration.
Still missing
  • No functional studies available for this synonymous variant
PS4 With an allele frequency of 44.6% in the general population (gnomAD), this variant is incompatible with enrichment in affected individuals for any rare Mendelian disease. No case-control studies demonstrating significant enrichment were identified. Details ▾Hide ▴
Evidence considered
  • gnomAD AF = 44.66% (v2.1)
  • 44.40% (v4.1)
  • variant is a common polymorphism present in nearly half the population.
Sources
PM1 This variant does not lie in a statistically significant mutational hotspot (cancerhotspots.org negative). Although located in exon 4 of CCND1, the variant is synonymous (p.Pro241=) and does not alter the cyclin D1 protein; no domain-level pathogenic evidence applies. Details ▾Hide ▴
Evidence considered
  • cancerhotspots.org: residue not significant
  • exact variant not listed
  • synonymous variant does not alter protein functional domains.
PM2 This variant is extremely common in gnomAD: AF = 44.66% in v2.1 (125,943/282,012 alleles, 29,329 homozygotes) and 44.40% in v4.1 (716,284/1,613,168 alleles, 162,210 homozygotes). Far exceeds the PM2 threshold of <0.1% allele frequency. Details ▾Hide ▴
Evidence considered
  • gnomAD v2.1 AF=44.66%
  • gnomAD v4.1 AF=44.40%
  • variant is a common polymorphism.
Sources
PP3 Multiple lines of computational evidence do not support a deleterious effect. SpliceAI max delta = 0.02 predicts no splicing impact. REVEL and BayesDel scores are unavailable for this synonymous variant, consistent with absence of predicted amino acid effect. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta = 0.02 (no predicted splicing impact)
  • synonymous variant with no amino acid change.
Sources
PP5 ClinVar reports this variant as Benign (Variation ID 13755), not Pathogenic. PP5 requires a reputable source to report the variant as pathogenic; the ClinVar classification is the opposite. Details ▾Hide ▴
Evidence considered
  • ClinVar classification: Benign
  • review status: criteria provided
  • single submitter.
Sources
BS3 No well-established in vitro or in vivo functional studies demonstrating no damaging effect for this specific variant. The variant is synonymous with no predicted splice impact, but no dedicated functional studies were identified. Details ▾Hide ▴
Evidence considered
  • No variant-specific functional studies identified.
Still missing
  • No dedicated functional studies available for this variant

Not assessed · 8 · no assessment recorded

PS2 No de novo data available for this variant. Details ▾Hide ▴
Still missing
  • No de novo testing data identified
PM6 No de novo data available for this variant. Details ▾Hide ▴
Still missing
  • No de novo testing data identified
PP1 No segregation data available for this variant. Details ▾Hide ▴
Still missing
  • No family segregation data identified
PP4 No patient phenotype or clinical data available for assessment. Details ▾Hide ▴
Still missing
  • No patient phenotype data available
BS4 No segregation data available to assess lack of cosegregation with disease. Details ▾Hide ▴
Still missing
  • No family segregation data identified
BP2 No data available on observations in trans with a known pathogenic variant. Details ▾Hide ▴
Still missing
  • No trans-phase observation data available
BP5 No data available. BP5 requires a case where an alternative molecular basis for disease was identified, excluding this variant. Details ▾Hide ▴
Still missing
  • No case data with alternative molecular basis identified
PS5 No independent data identifying this variant as pathogenic from a source not already reviewed. Details ▾Hide ▴
Still missing
  • No independent pathogenic assertion identified
Not applicable · 5· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/ASynonymous variant (NP_444284.1:p.(Pro241=)) does not fall into any null-variant bucket. pvs1_variant_assessment confirms variant_bucket='other' and apply_generic_pvs1_framework=false. Details ▾Hide ▴
Evidence considered
  • Synonymous substitution c.723G>A produces no amino acid change
  • not a nonsense
  • frameshift
  • or canonical splice site variant.
Sources
pvs1_variant_assessmentpvs1_gene_context
PS1 N/ASynonymous variant produces no amino acid change; there is no same-amino-acid pathogenic comparator possible. Details ▾Hide ▴
Evidence considered
  • Synonymous variant (p.Pro241=) does not alter the amino acid sequence.
PM5 N/ASynonymous variant (p.Pro241=) with no alternative missense change at this residue. pm5_candidates.json confirms: unable to confirm classic same-residue PM5 semantics. Details ▾Hide ▴
Evidence considered
  • Synonymous variant
  • no missense comparator exists at residue 241.
Sources
pm5_candidates
PP2 N/AThis is a synonymous variant, not a missense variant. PP2 specifically applies to missense variants in genes where missense variants are a known mechanism and benign missense variation is rare. Details ▾Hide ▴
Evidence considered
  • Synonymous variant (p.Pro241=) is not a missense change.
BP1 N/AThis is a synonymous variant, not a missense variant. BP1 specifically applies to missense variants in genes where primarily truncating variants are known to cause disease. Details ▾Hide ▴
Evidence considered
  • Synonymous variant (p.Pro241=) is not a missense change.

Identifiers

Gene
CCND1
Transcript
NM_053056.3
Coding (HGVS c.)
NM_053056.3:c.723G>A
Protein (HGVS p.)
NP_444284.1:p.(Pro241=)
GRCh38
chr11:69648142 G>A
GRCh37
chr11:69462910 G>A
ClinVar
13755
COSMIC
COSV57118864

Gene diagram

Every interpreted variant in CCND1, mapped onto the exon structure of NM_053056.3. Select a row to find it on the plot.

CCND1NM_053056.3
Fetching transcript structure from UCSC…
gnomAD v4.1 716,284 / 1,613,168 alleles AF 0.444 · 162210 homozygotes · FAF 0.52
gnomAD v2.1 125,943 / 282,012 alleles AF 0.447 · 29329 homozygotes · FAF 0.56
gnomAD-Canada v1.0 Allele count data not recorded

By genetic ancestry

gnomAD v4.1

AF 0.44 · 716284 / 1,613,168 alleles · 162210 hom · FAF 0.52
East Asian23571 / 44,848 0.536204 hom
South Asian47620 / 91,060 0.5212712 hom
Middle Eastern3108 / 6,058 0.51824 hom
European (Finnish)30437 / 63,546 0.487327 hom
Remaining individuals28397 / 62,486 0.456540 hom
European (non-Finnish)530242 / 1,179,672 0.45119379 hom
Ashkenazi Jewish13148 / 29,600 0.442908 hom
Amish360 / 912 0.3968 hom
Admixed American23115 / 59,992 0.394492 hom
African/African American16286 / 74,994 0.221756 hom

gnomAD v2.1

AF 0.45 · 125943 / 282,012 alleles · 29329 hom · FAF 0.56
East Asian11294 / 19,922 0.573160 hom
South Asian15976 / 30,590 0.524244 hom
European (Finnish)12189 / 25,070 0.493030 hom
European (non-Finnish)59874 / 128,642 0.4713989 hom
Remaining individuals3328 / 7,198 0.46807 hom
Ashkenazi Jewish4635 / 10,328 0.451034 hom
Admixed American13309 / 35,362 0.382483 hom
African/African American5338 / 24,900 0.21582 hom

gnomAD-Canada

AF not recorded · ? / ? alleles

Statements

gnomAD v4.1

This variant is present in gnomAD v4.1 (AF= 0.444023; MAF= 44.40232%, 716284/1613168 alleles, homozygotes = 162210) and has highest observed frequency in the East Asian population (AF= 0.525575; MAF= 52.55753%, 23571/44848 alleles, homozygotes = 6204); grpmax FAF= 0.519956.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 0.446587; MAF= 44.65874%, 125943/282012 alleles, homozygotes = 29329) and has highest observed frequency in the East Asian population (AF= 0.566911; MAF= 56.69110%, 11294/19922 alleles, homozygotes = 3160); grpmax FAF= 0.559639.

gnomAD-Canada

This variant is present in gnomAD-Canada v1.0 (AF= 0.4660823170731707, 8561/18368 alleles, homozygotes = 2065).

Open the gnomAD-Canada detail page →

SpliceAI and Pangolin

SpliceAI acceptor lossat +182 bp
0.020
SpliceAI acceptor gainat -472 bp
0.000
SpliceAI donor lossat -392 bp
0.000
SpliceAI donor gainat +4 bp
0.000
Pangolin splice lossmagnitude shown
-0.030
Pangolin splice gain
0.010

Other predictors

REVEL
Not available
BayesDel
Not available

How the predictions were used

BP4 SupportingMultiple lines of computational evidence suggest no impact on the gene product. SpliceAI max delta = 0.02 predicts no splicing effect. The variant is synonymous (p.Pro241=) and does not alter the amino acid sequence. REVEL and BayesDel scores are unavailable, as expected for a synonymous variant with no amino acid change. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta score = 0.02 (no predicted splicing impact)
  • synonymous variant (p.Pro241=) with no amino acid change.
Sources
BP7 SupportingSynonymous variant (p.Pro241=) at a nucleotide position where SpliceAI predicts no splicing impact (max delta = 0.02). The variant does not alter the amino acid sequence and is not predicted to affect splicing, meeting BP7 criteria. Details ▾Hide ▴
Evidence considered
  • Synonymous substitution p.Pro241= with no amino acid change
  • SpliceAI max delta = 0.02 (no splicing impact predicted).
Sources
PP3 Multiple lines of computational evidence do not support a deleterious effect. SpliceAI max delta = 0.02 predicts no splicing impact. REVEL and BayesDel scores are unavailable for this synonymous variant, consistent with absence of predicted amino acid effect. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta = 0.02 (no predicted splicing impact)
  • synonymous variant with no amino acid change.
Sources

Statement

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02).

7 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.

Recorded publications

  • Effects of cyclin D1 polymorphism on age of onset of hereditary nonpolyposis colorectal cancer.
    Kong S et al. · 2000
    Reports that a common polymorphism in the cyclin D1 gene enhances alternate splicing and modifies age of onset of hereditary nonpolyposis colorectal cancer. Discusses the CCND1 G870A splice variant polymorphism, not NM_053056.3:c.723G>A.
    Does not name this variant
    PMID 10667569 ↗
  • Identification of cyclin D1 and other novel targets for the von Hippel-Lindau tumor suppressor gene by expression array analysis and investigation of cyclin D1 genotype as a modifier in von Hippel-Lindau disease.
    Zatyka M et al. · 2002
    Investigates cyclin D1 as a target of VHL and examines cyclin D1 genotype as a modifier in von Hippel-Lindau disease. Discusses the CCND1 polymorphism in the context of disease modification, not NM_053056.3:c.723G>A.
    Does not name this variant
    PMID 12097293 ↗
  • Cyclin D1-Cdk4 controls glucose metabolism independently of cell cycle progression.
    Lee Y et al. · 2014
    Demonstrates that cyclin D1-Cdk4 controls glucose metabolism independently of cell cycle progression through PGC-1alpha acetylation. A functional study of cyclin D1 protein biology; does not discuss any specific CCND1 germline variant.
    Does not name this variant
    PMID 24870244 ↗
  • Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
    Richards S et al. · 2015
    ACMG/AMP standards and guidelines for interpretation of sequence variants. Provides the framework used for this assessment but does not discuss any specific variant.
    Does not name this variant
    PMID 25741868 ↗
  • Pan-cancer repository of validated natural and cryptic mRNA splicing mutations.
    Shirley BC et al. · 2018
    Pan-cancer repository of validated mRNA splicing mutations from TCGA and ICGC datasets. A bioinformatic resource; does not discuss NM_053056.3:c.723G>A specifically.
    Does not name this variant
    PMID 31275557 ↗
  • Cyclin D1 polymorphism and increased risk of colorectal cancer at young age.
    Kong S et al. · 2001
    Examines cyclin D1 polymorphism and increased risk of colorectal cancer at young age. Discusses the CCND1 G870A polymorphism, not NM_053056.3:c.723G>A.
    Does not name this variant
    PMID 11459873 ↗
  • The CCND1 c.870G&gt;A polymorphism is a risk factor for t(11;14)(q13;q32) multiple myeloma.
    Weinhold N et al. · 2013
    Reports that the CCND1 c.870G>A polymorphism is a risk factor for t(11;14)(q13;q32) multiple myeloma. This paper studies c.870G>A, a different variant from NM_053056.3:c.723G>A.
    Does not name this variant
    PMID 23502783 ↗
    Quoted passage
    These translocations cause transcriptional activation of FGFR3/MMSET and CCND1 which contribute to MM biology.

    Full text reviewed; paper discusses c.870G>A (rs603965), not c.723G>A.

Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.

All source links

Statements for reports

The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.

gnomAD v4.1

This variant is present in gnomAD v4.1 (AF= 0.444023; MAF= 44.40232%, 716284/1613168 alleles, homozygotes = 162210) and has highest observed frequency in the East Asian population (AF= 0.525575; MAF= 52.55753%, 23571/44848 alleles, homozygotes = 6204); grpmax FAF= 0.519956.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 0.446587; MAF= 44.65874%, 125943/282012 alleles, homozygotes = 29329) and has highest observed frequency in the East Asian population (AF= 0.566911; MAF= 56.69110%, 11294/19922 alleles, homozygotes = 3160); grpmax FAF= 0.559639.

gnomAD-Canada

This variant is present in gnomAD-Canada v1.0 (AF= 0.4660823170731707, 8561/18368 alleles, homozygotes = 2065).

ClinVar

This variant has been reported in ClinVar as Benign (2 clinical laboratories). (ClinVarID = 13755)

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02).

Functional

OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.

Somatic

This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV57118864, n = 79 times).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.