rs4530754

Variant names:

• chr5-123519722-G-A
• rs4530754
• NM_001364140.2:c.-248+7152G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-123519722-G-A
• chr5-123519722-G-C
• chr5-123519722-G-T

Variant summary

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

The NM_001364140.2(CSNK1G3):​c.-248+7152G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 151,994 control chromosomes in the GnomAD database, including 28,932 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 0.60 (28932 hom., cov: 31)
• Consequence: CSNK1G3 NM_001364140.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736
• Publications: 65 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSNK1G3	NM_001364140.2	c.-248+7152G>A		intron_variant	Intron 1 of 13	ENST00000696905.1	NP_001351069.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSNK1G3	ENST00000696905.1	c.-248+7152G>A		intron_variant	Intron 1 of 13		NM_001364140.2	ENSP00000512966.1

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91584 AN: 151876 Hom.: 28885 Cov.: 31

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.603 AC: 91684 AN: 151994 Hom.: 28932 Cov.: 31 AF XY: 0.597 AC XY: 44351 AN XY: 74290

African (AFR) AF: 0.789 AC: 32737 AN: 41474

American (AMR) AF: 0.546 AC: 8330 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2149 AN: 3470

East Asian (EAS) AF: 0.334 AC: 1726 AN: 5168

South Asian (SAS) AF: 0.432 AC: 2076 AN: 4804

European-Finnish (FIN) AF: 0.496 AC: 5224 AN: 10534

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.548 AC: 37251 AN: 67958

Other (OTH) AF: 0.629 AC: 1329 AN: 2114

Alfa AF: 0.555 Hom.: 50548

Bravo AF: 0.618

Asia WGS AF: 0.433 AC: 1505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.23
DANN	Benign	0.61
PhyloP100		-0.74
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4530754; hg19: chr5-122855416;