chr9-89316143-T-A

Position:

• chr9-89316143-T-A

Variant summary

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

The NM_001827.3(CKS2):​c.188-230T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.025 in 152,240 control chromosomes in the GnomAD database, including 160 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 0.025 (160 hom., cov: 33)
• Consequence: CKS2 NM_001827.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

Genes affected

CKS2 (HGNC:2000): (CDC28 protein kinase regulatory subunit 2) CKS2 protein binds to the catalytic subunit of the cyclin dependent kinases and is essential for their biological function. The CKS2 mRNA is found to be expressed in different patterns through the cell cycle in HeLa cells, which reflects specialized role for the encoded protein. [provided by RefSeq, Jul 2008]

ACMG classification

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 = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CKS2	NM_001827.3	c.188-230T>A		intron_variant		ENST00000314355.7	NP_001818.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CKS2	ENST00000314355.7	c.188-230T>A		intron_variant		1	NM_001827.3	ENSP00000364976.3

Frequencies

GnomAD3 genomes AF: 0.0250 AC: 3797 AN: 152122 Hom.: 161 Cov.: 33

Gnomad AFR AF: 0.0343

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0140

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.00141

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.00678

Gnomad OTH AF: 0.0211

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0250 AC: 3801 AN: 152240 Hom.: 160 Cov.: 33 AF XY: 0.0270 AC XY: 2008 AN XY: 74422

Gnomad4 AFR AF: 0.0343

Gnomad4 AMR AF: 0.0139

Gnomad4 ASJ AF: 0.0300

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.00141

Gnomad4 NFE AF: 0.00680

Gnomad4 OTH AF: 0.0213

Alfa AF: 0.00254 Hom.: 0

Bravo AF: 0.0242

Asia WGS AF: 0.133 AC: 460 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.29
DANN	Benign	0.74

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: rs3211690; hg19: chr9-91931058;