Variant chr10-60794005-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000395284.8(CDK1):c.*30A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.763 in 1,041,966 control chromosomes in the GnomAD database, including 304,787 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.75 ( 43186 hom., cov: 32)

Exomes 𝑓: 0.77 ( 261601 hom. )

Consequence

CDK1
ENST00000395284.8 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0690

Variant links:

Genes affected

CDK1 (HGNC:1722): (cyclin dependent kinase 1) The protein encoded by this gene is a member of the Ser/Thr protein kinase family. This protein is a catalytic subunit of the highly conserved protein kinase complex known as M-phase promoting factor (MPF), which is essential for G2/M phase transitions of eukaryotic cell cycle. Mitotic cyclins stably associate with this protein and function as regulatory subunits. The kinase activity of this protein is controlled by cyclin accumulation and destruction through the cell cycle. The phosphorylation and dephosphorylation of this protein also play important regulatory roles in cell cycle control. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2023]

CDK1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
CDK1	NM_001786.5 linkuse as main transcript	c.*30A>G	3_prime_UTR_variant	8/8	ENST00000395284.8	NP_001777.1
CDK1	NM_001320918.1 linkuse as main transcript	c.*30A>G	3_prime_UTR_variant	8/8		NP_001307847.1
CDK1	NM_033379.5 linkuse as main transcript	c.*30A>G	3_prime_UTR_variant	7/7		NP_203698.1
CDK1	XM_005270303.4 linkuse as main transcript	c.*30A>G	3_prime_UTR_variant	8/8		XP_005270360.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDK1	ENST00000395284.8 linkuse as main transcript	c.*30A>G	3_prime_UTR_variant	8/8	1	NM_001786.5	ENSP00000378699	P3	P06493-1
CDK1	ENST00000373809.2 linkuse as main transcript	c.*30A>G	3_prime_UTR_variant	6/6	1		ENSP00000362915		P06493-2
CDK1	ENST00000448257.6 linkuse as main transcript	c.*30A>G	3_prime_UTR_variant	8/8	1		ENSP00000397973	A1
CDK1	ENST00000316629.8 linkuse as main transcript	c.*30A>G	3_prime_UTR_variant	7/7	5		ENSP00000325970		P06493-2

Frequencies

GnomAD3 genomes

AF:

0.752

AC:

114169

AN:

151766

Hom.:

43158

Cov.:

show subpopulations

Gnomad AFR

AF:

0.698

Gnomad AMI

AF:

0.766

Gnomad AMR

AF:

0.776

Gnomad ASJ

AF:

0.773

Gnomad EAS

AF:

0.838

Gnomad SAS

AF:

0.800

Gnomad FIN

AF:

0.852

Gnomad MID

AF:

0.775

Gnomad NFE

AF:

0.753

Gnomad OTH

AF:

0.760

GnomAD3 exomes

AF:

0.779

AC:

137089

AN:

175962

Hom.:

53589

AF XY:

0.780

AC XY:

76405

AN XY:

97918

show subpopulations

Gnomad AFR exome

AF:

0.692

Gnomad AMR exome

AF:

0.782

Gnomad ASJ exome

AF:

0.778

Gnomad EAS exome

AF:

0.851

Gnomad SAS exome

AF:

0.802

Gnomad FIN exome

AF:

0.846

Gnomad NFE exome

AF:

0.761

Gnomad OTH exome

AF:

0.768

GnomAD4 exome

AF:

0.765

AC:

681143

AN:

890082

Hom.:

261601

Cov.:

AF XY:

0.766

AC XY:

355273

AN XY:

464090

show subpopulations

Gnomad4 AFR exome

AF:

0.702

Gnomad4 AMR exome

AF:

0.787

Gnomad4 ASJ exome

AF:

0.783

Gnomad4 EAS exome

AF:

0.803

Gnomad4 SAS exome

AF:

0.802

Gnomad4 FIN exome

AF:

0.845

Gnomad4 NFE exome

AF:

0.753

Gnomad4 OTH exome

AF:

0.773

GnomAD4 genome

AF:

0.752

AC:

114254

AN:

151884

Hom.:

43186

Cov.:

AF XY:

0.758

AC XY:

56280

AN XY:

74238

show subpopulations

Gnomad4 AFR

AF:

0.698

Gnomad4 AMR

AF:

0.775

Gnomad4 ASJ

AF:

0.773

Gnomad4 EAS

AF:

0.837

Gnomad4 SAS

AF:

0.800

Gnomad4 FIN

AF:

0.852

Gnomad4 NFE

AF:

0.753

Gnomad4 OTH

AF:

0.757

Alfa

AF:

0.751

Hom.:

19429

Bravo

AF:

0.745

Asia WGS

AF:

0.776

AC:

2685

AN:

3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.0

DANN

Benign

0.56

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over