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GeneBe

rs2448343

Variant summary

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

The NM_001786.5(CDK1):c.-25-255A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 151,412 control chromosomes in the GnomAD database, including 27,361 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 0.60 ( 27361 hom., cov: 32)

Consequence

CDK1
NM_001786.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0560
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]

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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=-0.69).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CDK1NM_001786.5 linkuse as main transcriptc.-25-255A>G intron_variant ENST00000395284.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CDK1ENST00000395284.8 linkuse as main transcriptc.-25-255A>G intron_variant 1 NM_001786.5 P3P06493-1

Frequencies

GnomAD3 genomes
AF:
0.597
AC:
90305
AN:
151296
Hom.:
27364
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.482
Gnomad AMI
AF:
0.533
Gnomad AMR
AF:
0.621
Gnomad ASJ
AF:
0.606
Gnomad EAS
AF:
0.762
Gnomad SAS
AF:
0.655
Gnomad FIN
AF:
0.680
Gnomad MID
AF:
0.653
Gnomad NFE
AF:
0.631
Gnomad OTH
AF:
0.621
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.597
AC:
90347
AN:
151412
Hom.:
27361
Cov.:
32
AF XY:
0.601
AC XY:
44498
AN XY:
74026
show subpopulations
Gnomad4 AFR
AF:
0.482
Gnomad4 AMR
AF:
0.621
Gnomad4 ASJ
AF:
0.606
Gnomad4 EAS
AF:
0.762
Gnomad4 SAS
AF:
0.654
Gnomad4 FIN
AF:
0.680
Gnomad4 NFE
AF:
0.631
Gnomad4 OTH
AF:
0.619
Alfa
AF:
0.598
Hom.:
12277
Bravo
AF:
0.585

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.69
Cadd
Benign
3.8
Dann
Benign
0.87

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: rs2448343; hg19: chr10-62539644; API