Variant 1-1637774-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_033486.3(CDK11B):c.1452C>T(p.Ile484=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000887 in 1,610,690 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0018 ( 4 hom., cov: 32)

Exomes 𝑓: 0.00079 ( 5 hom. )

Consequence

CDK11B
NM_033486.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.789

Variant links:

Genes affected

CDK11B (HGNC:1729): (cyclin dependent kinase 11B) This gene encodes a member of the serine/threonine protein kinase family. Members of this kinase family are known to be essential for eukaryotic cell cycle control. Due to a segmental duplication, this gene shares very high sequence identity with a neighboring gene. These two genes are frequently deleted or altered in neuroblastoma. The protein kinase encoded by this gene can be cleaved by caspases and may play a role in cell apoptosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2014]

CDK11B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.31).

BP6

Variant 1-1637774-G-A is Benign according to our data. Variant chr1-1637774-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2638050.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.789 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDK11B	NM_033486.3 linkuse as main transcript	c.1452C>T	p.Ile484=	synonymous_variant	13/20	ENST00000341832.11	NP_277021.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDK11B	ENST00000341832.11 linkuse as main transcript	c.1452C>T	p.Ile484=	synonymous_variant	13/20	1	NM_033486.3	ENSP00000463048	P1	P21127-2

Frequencies

GnomAD3 genomes

AF:

0.00173

AC:

262

AN:

151214

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00297

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00144

Gnomad ASJ

AF:

0.00346

Gnomad EAS

AF:

0.000579

Gnomad SAS

AF:

0.00457

Gnomad FIN

AF:

0.000188

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00105

Gnomad OTH

AF:

0.00385

GnomAD3 exomes

AF:

0.000370

AC:

AN:

248534

Hom.:

AF XY:

0.000401

AC XY:

AN XY:

134804

show subpopulations

Gnomad AFR exome

AF:

0.000259

Gnomad AMR exome

AF:

0.000290

Gnomad ASJ exome

AF:

0.00120

Gnomad EAS exome

AF:

0.000501

Gnomad SAS exome

AF:

0.00102

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000195

Gnomad OTH exome

AF:

0.000664

GnomAD4 exome

AF:

0.000791

AC:

1154

AN:

1459360

Hom.:

Cov.:

AF XY:

0.000882

AC XY:

640

AN XY:

725902

show subpopulations

Gnomad4 AFR exome

AF:

0.00151

Gnomad4 AMR exome

AF:

0.000739

Gnomad4 ASJ exome

AF:

0.00438

Gnomad4 EAS exome

AF:

0.00338

Gnomad4 SAS exome

AF:

0.00244

Gnomad4 FIN exome

AF:

0.000112

Gnomad4 NFE exome

AF:

0.000463

Gnomad4 OTH exome

AF:

0.00140

GnomAD4 genome

AF:

0.00182

AC:

275

AN:

151330

Hom.:

Cov.:

AF XY:

0.00182

AC XY:

135

AN XY:

74022

show subpopulations

Gnomad4 AFR

AF:

0.00301

Gnomad4 AMR

AF:

0.00144

Gnomad4 ASJ

AF:

0.00346

Gnomad4 EAS

AF:

0.000580

Gnomad4 SAS

AF:

0.00457

Gnomad4 FIN

AF:

0.000188

Gnomad4 NFE

AF:

0.00105

Gnomad4 OTH

AF:

0.00905

Alfa

AF:

0.00190

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

CDK11B: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.31

CADD

Benign

2.1

DANN

Benign

0.91

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over