9-89314992-T-G

Position:

• chr9-89314992-T-G

Variant summary

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

The NM_001827.3(CKS2):​c.60-178T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0406 in 152,294 control chromosomes in the GnomAD database, including 203 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 0.041 (203 hom., cov: 32)
• Consequence: CKS2 NM_001827.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CKS2	NM_001827.3	c.60-178T>G		intron_variant		ENST00000314355.7	NP_001818.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CKS2	ENST00000314355.7	c.60-178T>G		intron_variant		1	NM_001827.3	ENSP00000364976.3

Frequencies

GnomAD3 genomes AF: 0.0407 AC: 6187 AN: 152176 Hom.: 203 Cov.: 32

Gnomad AFR AF: 0.00926

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0286

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.0124

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0588

Gnomad OTH AF: 0.0301

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

GnomAD4 genome AF: 0.0406 AC: 6184 AN: 152294 Hom.: 203 Cov.: 32 AF XY: 0.0410 AC XY: 3056 AN XY: 74474

Gnomad4 AFR AF: 0.00924

Gnomad4 AMR AF: 0.0286

Gnomad4 ASJ AF: 0.0121

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0118

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.0588

Gnomad4 OTH AF: 0.0298

Alfa AF: 0.0466 Hom.: 119

Bravo AF: 0.0336

Asia WGS AF: 0.00520 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.2
DANN	Benign	0.73

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: rs3211684; hg19: chr9-91929907;