9-89316143-T-A

Variant names:

• chr9-89316143-T-A
• rs3211690
• NM_001827.3:c.188-230T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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]

ENSG00000309658 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001827.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CKS2	NM_001827.3	MANE Select	c.188-230T>A		intron	N/A	NP_001818.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CKS2	ENST00000314355.7	TSL:1 MANE Select	c.188-230T>A		intron	N/A	ENSP00000364976.3
	CKS2	ENST00000940742.1		c.227-230T>A		intron	N/A	ENSP00000610801.1
	CKS2	ENST00000940741.1		c.170-230T>A		intron	N/A	ENSP00000610800.1

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

African (AFR) AF: 0.0343 AC: 1427 AN: 41570

American (AMR) AF: 0.0139 AC: 213 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0300 AC: 104 AN: 3468

East Asian (EAS) AF: 0.162 AC: 839 AN: 5172

South Asian (SAS) AF: 0.143 AC: 690 AN: 4822

European-Finnish (FIN) AF: 0.00141 AC: 15 AN: 10612

Middle Eastern (MID) AF: 0.0205 AC: 6 AN: 292

European-Non Finnish (NFE) AF: 0.00680 AC: 462 AN: 67990

Other (OTH) AF: 0.0213 AC: 45 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.29
DANN	Benign	0.74
PhyloP100		-1.9
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

Other links and lift over

dbSNP: rs3211690; hg19: chr9-91931058;