rs1904416

Variant names:

• chr10-60783609-C-T
• rs1904416
• NM_001786.5:c.38-1096C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001786.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDK1	NM_001786.5	MANE Select	c.38-1096C>T		intron	N/A	NP_001777.1	P06493-1
	CDK1	NM_001320918.1		c.38-1096C>T		intron	N/A	NP_001307847.1	P06493-1
	CDK1	NM_033379.5		c.38-1096C>T		intron	N/A	NP_203698.1	P06493-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDK1	ENST00000395284.8	TSL:1 MANE Select	c.38-1096C>T		intron	N/A	ENSP00000378699.3	P06493-1
	CDK1	ENST00000448257.6	TSL:1	c.38-1096C>T		intron	N/A	ENSP00000397973.2	A0A024QZP7
	CDK1	ENST00000373809.2	TSL:1	c.38-1096C>T		intron	N/A	ENSP00000362915.2	P06493-2

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

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.667 AC: 8 AN: 12

Other (OTH) AF: 0.667 AC: 4 AN: 6

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

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.30
DANN	Benign	0.68
PhyloP100		-0.53
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1904416;

hg19: chr10-62543367;