12-12717807-CGAGA-C

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BS1_SupportingBS2

The NM_004064.5(CDKN1B):​c.-29_-26delAGAG 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

Scores

Not classified

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2U:3B:5

Conservation

PhyloP100: 1.65
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -5 ACMG points.

BS1
Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.000388 (59/152226) while in subpopulation AMR AF = 0.00098 (15/15302). AF 95% confidence interval is 0.000604. There are 0 homozygotes in GnomAd4. There are 29 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position FAILED quality control check. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
High AC in GnomAd4 at 59 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CDKN1BNM_004064.5 linkc.-29_-26delAGAG 5_prime_UTR_variant Exon 1 of 3 ENST00000228872.9 NP_004055.1 P46527Q6I9V6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CDKN1BENST00000228872 linkc.-29_-26delAGAG 5_prime_UTR_variant Exon 1 of 3 1 NM_004064.5 ENSP00000228872.4 P46527

Frequencies

GnomAD3 genomes
AF:
0.000388
AC:
59
AN:
152108
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000169
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000982
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000515
Gnomad OTH
AF:
0.000956
GnomAD2 exomes
AF:
0.000376
AC:
92
AN:
244842
AF XY:
0.000463
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000522
Gnomad ASJ exome
AF:
0.000101
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000643
Gnomad OTH exome
AF:
0.000333
GnomAD4 exome
AF:
0.000581
AC:
846
AN:
1456964
Hom.:
1
AF XY:
0.000584
AC XY:
423
AN XY:
724762
show subpopulations
Gnomad4 AFR exome
AF:
0.0000898
AC:
3
AN:
33412
Gnomad4 AMR exome
AF:
0.000604
AC:
27
AN:
44718
Gnomad4 ASJ exome
AF:
0.00
AC:
0
AN:
26124
Gnomad4 EAS exome
AF:
0.00
AC:
0
AN:
39688
Gnomad4 SAS exome
AF:
0.0000116
AC:
1
AN:
86178
Gnomad4 FIN exome
AF:
0.000177
AC:
9
AN:
50752
Gnomad4 NFE exome
AF:
0.000699
AC:
777
AN:
1111694
Gnomad4 Remaining exome
AF:
0.000399
AC:
24
AN:
60146
Heterozygous variant carriers
0
48
96
145
193
241
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
28
56
84
112
140
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.000388
AC:
59
AN:
152226
Hom.:
0
Cov.:
33
AF XY:
0.000390
AC XY:
29
AN XY:
74424
show subpopulations
Gnomad4 AFR
AF:
0.000169
AC:
0.000168537
AN:
0.000168537
Gnomad4 AMR
AF:
0.000980
AC:
0.000980264
AN:
0.000980264
Gnomad4 ASJ
AF:
0.00
AC:
0
AN:
0
Gnomad4 EAS
AF:
0.00
AC:
0
AN:
0
Gnomad4 SAS
AF:
0.00
AC:
0
AN:
0
Gnomad4 FIN
AF:
0.00
AC:
0
AN:
0
Gnomad4 NFE
AF:
0.000515
AC:
0.000514645
AN:
0.000514645
Gnomad4 OTH
AF:
0.000946
AC:
0.000946074
AN:
0.000946074
Heterozygous variant carriers
0
4
7
11
14
18
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.000564
Hom.:
0
Bravo
AF:
0.000548

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
Oct 08, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Jan 01, 2019
Institute of Human Genetics, University of Leipzig Medical Center
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Mar 01, 2012
OMIM
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:literature only

- -

not specified Uncertain:2
Mar 04, 2025
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

May 04, 2022
Mendelics
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

not provided Uncertain:1Benign:1
Sep 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

CDKN1B: PS3:Moderate, BP4, BS1 -

Jun 13, 2024
GeneDx
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing

Published functional studies demonstrate a damaging effect: decreased transcriptional activity, reduced p27 mRNA, and increased cytoplasmic localization (PMID: 22129891, 25645465, 27038812); Identified in patients with clinical features of Multiple Endocrine Neoplasia syndrome type 4 (MEN4) in published literature, but inherited from an unaffected parent in at least one family (PMID: 22129891, 25645465, 27038812, 32232325); 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, 35355569, 30990521, 36520683, 22129891) -

Primary hyperparathyroidism Pathogenic:1
Jan 01, 2015
Endocrine Unit 2, University Hospital of Pisa
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:in vitro;research

- -

CDKN1B-related disorder Benign:1
Feb 16, 2024
PreventionGenetics, part of Exact Sciences
Significance:Likely benign
Review Status:no assertion criteria provided
Collection Method:clinical testing

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
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
Mutation Taster
=299/1
disease causing (ClinVar)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs774454456; hg19: chr12-12870741; API