rs869312166
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_004064.5(CDKN1B):c.-29_-26del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000562 in 1,609,190 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00039 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00058 ( 1 hom. )
Consequence
CDKN1B
NM_004064.5 5_prime_UTR
NM_004064.5 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.65
Genes affected
CDKN1B (HGNC:1785): (cyclin dependent kinase inhibitor 1B) This gene encodes a cyclin-dependent kinase inhibitor, which shares a limited similarity with CDK inhibitor CDKN1A/p21. The encoded protein binds to and prevents the activation of cyclin E-CDK2 or cyclin D-CDK4 complexes, and thus controls the cell cycle progression at G1. The degradation of this protein, which is triggered by its CDK dependent phosphorylation and subsequent ubiquitination by SCF complexes, is required for the cellular transition from quiescence to the proliferative state. Mutations in this gene are associated with multiple endocrine neoplasia type IV (MEN4). [provided by RefSeq, Apr 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP6
?
Variant 12-12717807-CGAGA-C is Benign according to our data. Variant chr12-12717807-CGAGA-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 217126.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=5, Uncertain_significance=3, Pathogenic=1}.
BS2
?
High AC in GnomAd4 at 59 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDKN1B | NM_004064.5 | c.-29_-26del | 5_prime_UTR_variant | 1/3 | ENST00000228872.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDKN1B | ENST00000228872.9 | c.-29_-26del | 5_prime_UTR_variant | 1/3 | 1 | NM_004064.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000388 AC: 59AN: 152108Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000376 AC: 92AN: 244842Hom.: 0 AF XY: 0.000463 AC XY: 62AN XY: 133778
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GnomAD4 exome AF: 0.000581 AC: 846AN: 1456964Hom.: 1 AF XY: 0.000584 AC XY: 423AN XY: 724762
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GnomAD4 genome ? AF: 0.000388 AC: 59AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.000390 AC XY: 29AN XY: 74424
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:2Uncertain:3Benign:5
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Multiple endocrine neoplasia type 4 Pathogenic:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | Jan 01, 2019 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 01, 2012 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2022 | - - |
not specified Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital | Jul 31, 2024 | - - |
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Nov 13, 2023 | Published functional studies demonstrate a damaging effect: decreased transcriptional activity, reduced p27 mRNA, and increased cytoplasmic localization (PMID: 22129891, 25645465, 27038812); Deleted nucleotides are not conserved across species; Also known as c.-32_-29del; This variant is associated with the following publications: (PMID: 27038812, 28824003, 25645465, 26054904, 27657986, 24819502, 30555957, 32232325, 34426522, 30065701, 22129891, 35355569, 30990521, 36520683) - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2023 | CDKN1B: PS3:Moderate, BP4, BS1 - |
Primary hyperparathyroidism Pathogenic:1
Pathogenic, flagged submission | in vitro;research | Endocrine Unit 2, University Hospital of Pisa | Jan 01, 2015 | - - |
CDKN1B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 16, 2024 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Multiple endocrine neoplasia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at