rs922433

Variant names:

• chr5-123602107-C-G
• rs922433
• NM_001364140.2:c.1186-2617C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001364140.2(CSNK1G3):​c.1186-2617C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,888 control chromosomes in the GnomAD database, including 4,286 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 0.24 (4286 hom., cov: 32)
• Consequence: CSNK1G3 NM_001364140.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322
• Publications: 1 publications found

Genes affected

CSNK1G3 (HGNC:2456): (casein kinase 1 gamma 3) This gene encodes a member of a family of serine/threonine protein kinases that phosphorylate caseins and other acidic proteins. A related protein in the African clawed frog participates in the transmission of Wnt/beta-catenin signaling. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]

CSNK1G3 Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001364140.2. 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
	CSNK1G3	NM_001364140.2	MANE Select	c.1186-2617C>G		intron	N/A	NP_001351069.1
	CSNK1G3	NM_001044723.3		c.1183-2617C>G		intron	N/A	NP_001038188.1
	CSNK1G3	NM_001437477.1		c.1180-2617C>G		intron	N/A	NP_001424406.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSNK1G3	ENST00000696905.1	MANE Select	c.1186-2617C>G		intron	N/A	ENSP00000512966.1
	CSNK1G3	ENST00000345990.9	TSL:1	c.1183-2617C>G		intron	N/A	ENSP00000334735.5
	CSNK1G3	ENST00000360683.6	TSL:1	c.1183-2617C>G		intron	N/A	ENSP00000353904.2

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35682 AN: 151770 Hom.: 4278 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.362

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.235 AC: 35700 AN: 151888 Hom.: 4286 Cov.: 32 AF XY: 0.234 AC XY: 17349 AN XY: 74234

African (AFR) AF: 0.244 AC: 10110 AN: 41414

American (AMR) AF: 0.206 AC: 3150 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1081 AN: 3472

East Asian (EAS) AF: 0.196 AC: 1010 AN: 5166

South Asian (SAS) AF: 0.224 AC: 1078 AN: 4808

European-Finnish (FIN) AF: 0.212 AC: 2239 AN: 10546

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.238 AC: 16134 AN: 67906

Other (OTH) AF: 0.246 AC: 520 AN: 2114

Alfa AF: 0.240 Hom.: 518

Bravo AF: 0.236

Asia WGS AF: 0.198 AC: 690 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.5
DANN	Benign	0.63
PhyloP100		-0.32
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: rs922433; hg19: chr5-122937801;