rs1059684

Positions:

• chr19-1981198-G-A
• chr19-1981198-G-C

Variant summary

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

The NM_001319.7(CSNK1G2):​c.*995G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,332 control chromosomes in the GnomAD database, including 3,500 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 0.17 (3498 hom., cov: 33)
  • Exomes 𝑓: 0.15 (2 hom.)
• Consequence: CSNK1G2 NM_001319.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.979

Genes affected

CSNK1G2 (HGNC:2455): (casein kinase 1 gamma 2) Enables protein serine/threonine kinase activity. Involved in peptidyl-serine phosphorylation. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSNK1G2	NM_001319.7	c.*995G>A		3_prime_UTR_variant	12/12	ENST00000255641.13	NP_001310.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSNK1G2	ENST00000255641.13	c.*995G>A		3_prime_UTR_variant	12/12	1	NM_001319.7	ENSP00000255641	P1

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25817 AN: 152086 Hom.: 3489 Cov.: 33

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0996

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0927

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0650

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0866

Gnomad OTH AF: 0.153

GnomAD4 exome AF: 0.148 AC: 19 AN: 128 Hom.: 2 Cov.: 0 AF XY: 0.148 AC XY: 16 AN XY: 108

Gnomad4 AFR exome AF: 0.375

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.333

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.130

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.170 AC: 25862 AN: 152204 Hom.: 3498 Cov.: 33 AF XY: 0.168 AC XY: 12473 AN XY: 74412

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.0995

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.0923

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0650

Gnomad4 NFE AF: 0.0866

Gnomad4 OTH AF: 0.152

Alfa AF: 0.0960 Hom.: 717

Bravo AF: 0.180

Asia WGS AF: 0.123 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.4
DANN	Benign	0.90
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.1

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: rs1059684; hg19: chr19-1981197;