NM_001364140.2:c.1179G>A

Variant names:

• chr5-123595128-G-A
• rs141285750
• NM_001364140.2:c.1179G>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Moderate BP6 BP7 BS2

The NM_001364140.2(CSNK1G3):​c.1179G>A​(p.Ser393Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0031 in 1,612,840 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.0021 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0032 (7 hom.)
• Consequence: CSNK1G3 NM_001364140.2 synonymous
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: 1.95
• Publications: 3 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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BP6: Variant 5-123595128-G-A is Benign according to our data. Variant chr5-123595128-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 3050578.Status of the report is no_assertion_criteria_provided, 0 stars.
• BP7: Synonymous conserved (PhyloP=1.95 with no splicing effect.
• BS2: High Homozygotes in GnomAdExome4 at 7 Unknown gene

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSNK1G3	NM_001364140.2	MANE Select	c.1179G>A	p.Ser393Ser	synonymous	Exon 11 of 14	NP_001351069.1	A0A8V8TKT3
	CSNK1G3	NM_001044723.3		c.1176G>A	p.Ser392Ser	synonymous	Exon 11 of 14	NP_001038188.1
	CSNK1G3	NM_001437477.1		c.1179G>A	p.Ser393Ser	splice_region synonymous	Exon 11 of 14	NP_001424406.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSNK1G3	ENST00000696905.1	MANE Select	c.1179G>A	p.Ser393Ser	synonymous	Exon 11 of 14	ENSP00000512966.1	A0A8V8TKT3
	CSNK1G3	ENST00000345990.9	TSL:1	c.1176G>A	p.Ser392Ser	synonymous	Exon 11 of 14	ENSP00000334735.5	Q9Y6M4-2
	CSNK1G3	ENST00000360683.6	TSL:1	c.1176G>A	p.Ser392Ser	synonymous	Exon 10 of 13	ENSP00000353904.2	Q9Y6M4-2

Frequencies

GnomAD3 genomes AF: 0.00208 AC: 316 AN: 151928 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000798

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000590

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.000189

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00381

Gnomad OTH AF: 0.00288

GnomAD2 exomes AF: 0.00175 AC: 438 AN: 250200 AF XY: 0.00175

Gnomad AFR exome AF: 0.000617

Gnomad AMR exome AF: 0.000553

Gnomad ASJ exome AF: 0.00249

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000926

Gnomad NFE exome AF: 0.00320

Gnomad OTH exome AF: 0.00295

GnomAD4 exome AF: 0.00320 AC: 4677 AN: 1460794 Hom.: 7 Cov.: 30 AF XY: 0.00314 AC XY: 2284 AN XY: 726702

African (AFR) AF: 0.000569 AC: 19 AN: 33402

American (AMR) AF: 0.000717 AC: 32 AN: 44606

Ashkenazi Jewish (ASJ) AF: 0.00172 AC: 45 AN: 26094

East Asian (EAS) AF: 0.00 AC: 0 AN: 39624

South Asian (SAS) AF: 0.000162 AC: 14 AN: 86206

European-Finnish (FIN) AF: 0.000244 AC: 13 AN: 53366

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5758

European-Non Finnish (NFE) AF: 0.00399 AC: 4438 AN: 1111406

Other (OTH) AF: 0.00192 AC: 116 AN: 60332

GnomAD4 genome AF: 0.00208 AC: 316 AN: 152046 Hom.: 0 Cov.: 32 AF XY: 0.00160 AC XY: 119 AN XY: 74332

African (AFR) AF: 0.000796 AC: 33 AN: 41480

American (AMR) AF: 0.000590 AC: 9 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.00173 AC: 6 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5172

South Asian (SAS) AF: 0.000208 AC: 1 AN: 4806

European-Finnish (FIN) AF: 0.000189 AC: 2 AN: 10574

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.00381 AC: 259 AN: 67966

Other (OTH) AF: 0.00285 AC: 6 AN: 2108

Alfa AF: 0.00270 Hom.: 1

Bravo AF: 0.00187

EpiCase AF: 0.00311

EpiControl AF: 0.00267

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	CSNK1G3-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	14
DANN	Benign	0.70
PhyloP100		2.0
Mutation Taster		=87/13	polymorphism

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: rs141285750; hg19: chr5-122930822;