rs1579036

Positions:

• chr5-123585409-G-A
• chr5-123585409-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001364140.2(CSNK1G3):​c.674-2659G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,824 control chromosomes in the GnomAD database, including 10,098 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 0.36 (10098 hom., cov: 32)
• Consequence: CSNK1G3 NM_001364140.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0500

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSNK1G3	NM_001364140.2	c.674-2659G>A		intron_variant		ENST00000696905.1	NP_001351069.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSNK1G3	ENST00000696905.1	c.674-2659G>A		intron_variant			NM_001364140.2	ENSP00000512966.1

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54596 AN: 151706 Hom.: 10079 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.360 AC: 54655 AN: 151824 Hom.: 10098 Cov.: 32 AF XY: 0.362 AC XY: 26826 AN XY: 74190

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.382

Alfa AF: 0.323 Hom.: 9847

Bravo AF: 0.364

Asia WGS AF: 0.348 AC: 1206 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.54

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

Publications

LitVar

Other links and lift over

dbSNP: rs1579036; hg19: chr5-122921103;