dbSNP rs1904416: CDK1:c.38-1096C>T (chr10-60783609-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001786.5(CDK1):c.38-1096C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 151,998 control chromosomes in the GnomAD database, including 41,756 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 0.74 ( 41751 hom., cov: 30)

Exomes 𝑓: 0.73 ( 5 hom. )

Consequence

CDK1
NM_001786.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.529

Publications

2 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDK1	NM_001786.5 link	c.38-1096C>T		intron_variant	Intron 2 of 7	ENST00000395284.8	NP_001777.1	P06493-1I6L9I5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDK1	ENST00000395284.8 link	c.38-1096C>T		intron_variant	Intron 2 of 7	1	NM_001786.5	ENSP00000378699.3		P06493-1

Frequencies

GnomAD3 genomes

AF:

0.739

AC:

112248

AN:

151858

Hom.:

41724

Cov.:

show subpopulations

Gnomad AFR

AF:

0.691

Gnomad AMI

AF:

0.687

Gnomad AMR

AF:

0.761

Gnomad ASJ

AF:

0.750

Gnomad EAS

AF:

0.838

Gnomad SAS

AF:

0.795

Gnomad FIN

AF:

0.845

Gnomad MID

AF:

0.750

Gnomad NFE

AF:

0.736

Gnomad OTH

AF:

0.743

GnomAD4 exome

AF:

0.727

AC:

AN:

Hom.:

Cov.:

AF XY:

0.714

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.667

AC:

AN:

Other (OTH)

AF:

0.667

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.450

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.739

AC:

112332

AN:

151976

Hom.:

41751

Cov.:

AF XY:

0.746

AC XY:

55415

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.691

AC:

28610

AN:

41406

American (AMR)

AF:

0.761

AC:

11619

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.750

AC:

2602

AN:

3468

East Asian (EAS)

AF:

0.838

AC:

4318

AN:

5154

South Asian (SAS)

AF:

0.795

AC:

3839

AN:

4826

European-Finnish (FIN)

AF:

0.845

AC:

8935

AN:

10568

Middle Eastern (MID)

AF:

0.745

AC:

219

AN:

294

European-Non Finnish (NFE)

AF:

0.736

AC:

50006

AN:

67972

Other (OTH)

AF:

0.740

AC:

1563

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1480

2961

4441

5922

7402

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

850

1700

2550

3400

4250

<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:

0.733

Hom.:

13882

Bravo

AF:

0.730

Asia WGS

AF:

0.774

AC:

2693

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.30

(source)

DANN

Benign

0.68

PhyloP100

-0.53

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over