9-89314992-T-G

Variant names:

• chr9-89314992-T-G
• rs3211684
• NM_001827.3:c.60-178T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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]

ACMG classification

Our verdict: Benign. The variant received -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.

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.60-178T>G		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.60-178T>G		intron	N/A	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

African (AFR) AF: 0.00924 AC: 384 AN: 41570

American (AMR) AF: 0.0286 AC: 437 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 42 AN: 3470

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5194

South Asian (SAS) AF: 0.0118 AC: 57 AN: 4826

European-Finnish (FIN) AF: 0.108 AC: 1144 AN: 10602

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0588 AC: 4001 AN: 68006

Other (OTH) AF: 0.0298 AC: 63 AN: 2114

Alfa AF: 0.0407 Hom.: 175

Bravo AF: 0.0336

Asia WGS AF: 0.00520 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.2
DANN	Benign	0.73
PhyloP100		-0.15
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: rs3211684; hg19: chr9-91929907;