rs4530754

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.95).
• 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/exons	MANE	UniProt
CSNK1G3	NM_001364140.2	c.-248+7152G>A		intron_variant		ENST00000696905.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSNK1G3	ENST00000696905.1	c.-248+7152G>A		intron_variant			NM_001364140.2	A1

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

Gnomad4 AFR AF: 0.789

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.629

Alfa AF: 0.553 Hom.: 34990

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4530754; hg19: chr5-122855416;