rs1904416

chr10-60783609-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CDK1	NM_001786.5	c.38-1096C>T		intron_variant		ENST00000395284.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDK1	ENST00000395284.8	c.38-1096C>T		intron_variant		1	NM_001786.5	P3

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112248 AN: 151858 Hom.: 41724 Cov.: 30

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: 16 AN: 22 Hom.: 5 Cov.: 0 AF XY: 0.714 AC XY: 10 AN XY: 14

Gnomad4 AFR exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.667

Gnomad4 OTH exome AF: 0.667

GnomAD4 genome AF: 0.739 AC: 112332 AN: 151976 Hom.: 41751 Cov.: 30 AF XY: 0.746 AC XY: 55415 AN XY: 74304

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.750

Gnomad4 EAS AF: 0.838

Gnomad4 SAS AF: 0.795

Gnomad4 FIN AF: 0.845

Gnomad4 NFE AF: 0.736

Gnomad4 OTH AF: 0.740

Alfa AF: 0.732 Hom.: 8224

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
Dann	Benign	0.68

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

Other links and lift over

dbSNP: rs1904416; hg19: chr10-62543367;