Variant 1-1641723-T-TTCC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_033486.3(CDK11B):c.945_947dupGGA(p.Glu316dup) variant causes a disruptive inframe insertion change. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00037 ( 2 hom., cov: 6)

Exomes 𝑓: 0.00053 ( 20 hom. )

Consequence

CDK11B
NM_033486.3 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.99

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:

CDK11B (HGNC:):

CDK11B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 1-1641723-T-TTCC is Benign according to our data. Variant chr1-1641723-T-TTCC is described in ClinVar as [Likely_benign]. Clinvar id is 3388587.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDK11B	NM_033486.3 linkuse as main transcript	c.945_947dupGGA	p.Glu316dup	disruptive_inframe_insertion	9/20	ENST00000341832.11	NP_277021.2	P21127-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDK11B	ENST00000341832.11 linkuse as main transcript	c.945_947dupGGA	p.Glu316dup	disruptive_inframe_insertion	9/20	1	NM_033486.3	ENSP00000463048.2		P21127-2

Frequencies

GnomAD3 genomes

AF:

0.000369

AC:

AN:

94856

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000193

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000200

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000285

Gnomad SAS

AF:

0.00239

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00424

Gnomad NFE

AF:

0.000387

Gnomad OTH

AF:

0.00159

GnomAD3 exomes

AF:

0.000796

AC:

AN:

27624

Hom.:

AF XY:

0.00101

AC XY:

AN XY:

13892

show subpopulations

Gnomad AFR exome

AF:

0.000292

Gnomad AMR exome

AF:

0.000609

Gnomad ASJ exome

AF:

0.00141

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00343

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000644

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000531

AC:

402

AN:

757756

Hom.:

Cov.:

AF XY:

0.000666

AC XY:

261

AN XY:

392022

show subpopulations

Gnomad4 AFR exome

AF:

0.0000653

Gnomad4 AMR exome

AF:

0.000457

Gnomad4 ASJ exome

AF:

0.000165

Gnomad4 EAS exome

AF:

0.0000325

Gnomad4 SAS exome

AF:

0.00344

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000284

Gnomad4 OTH exome

AF:

0.000539

GnomAD4 genome

AF:

0.000369

AC:

AN:

94856

Hom.:

Cov.:

AF XY:

0.000398

AC XY:

AN XY:

45190

show subpopulations

Gnomad4 AFR

AF:

0.000193

Gnomad4 AMR

AF:

0.000200

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000285

Gnomad4 SAS

AF:

0.00240

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000387

Gnomad4 OTH

AF:

0.00159

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

Sep 01, 2024

CDK11B: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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