19-1978272-C-T

Variant names:

• chr19-1978272-C-T
• rs740423
• NM_001319.7:c.188-33C>T

Variant summary

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

The NM_001319.7(CSNK1G2):​c.188-33C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 1,611,286 control chromosomes in the GnomAD database, including 12,183 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 (3385 hom., cov: 32)
  • Exomes 𝑓: 0.098 (8798 hom.)
• Consequence: CSNK1G2 NM_001319.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSNK1G2	NM_001319.7	c.188-33C>T		intron_variant	Intron 2 of 11	ENST00000255641.13	NP_001310.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSNK1G2	ENST00000255641.13	c.188-33C>T		intron_variant	Intron 2 of 11	1	NM_001319.7	ENSP00000255641.7

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25411 AN: 151870 Hom.: 3380 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0972

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0936

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0648

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0866

Gnomad OTH AF: 0.151

GnomAD3 exomes AF: 0.108 AC: 27018 AN: 249838 Hom.: 2192 AF XY: 0.104 AC XY: 14073 AN XY: 135498

Gnomad AFR exome AF: 0.379

Gnomad AMR exome AF: 0.0762

Gnomad ASJ exome AF: 0.143

Gnomad EAS exome AF: 0.0894

Gnomad SAS exome AF: 0.119

Gnomad FIN exome AF: 0.0653

Gnomad NFE exome AF: 0.0853

Gnomad OTH exome AF: 0.0906

GnomAD4 exome AF: 0.0978 AC: 142706 AN: 1459298 Hom.: 8798 Cov.: 35 AF XY: 0.0976 AC XY: 70884 AN XY: 725966

Gnomad4 AFR exome AF: 0.391

Gnomad4 AMR exome AF: 0.0762

Gnomad4 ASJ exome AF: 0.144

Gnomad4 EAS exome AF: 0.0807

Gnomad4 SAS exome AF: 0.119

Gnomad4 FIN exome AF: 0.0643

Gnomad4 NFE exome AF: 0.0888

Gnomad4 OTH exome AF: 0.108

GnomAD4 genome AF: 0.167 AC: 25443 AN: 151988 Hom.: 3385 Cov.: 32 AF XY: 0.165 AC XY: 12287 AN XY: 74316

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.0970

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.0933

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0648

Gnomad4 NFE AF: 0.0866

Gnomad4 OTH AF: 0.150

Alfa AF: 0.0894 Hom.: 1044

Bravo AF: 0.177

Asia WGS AF: 0.121 AC: 421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.98
DANN	Benign	0.48
RBP_binding_hub_radar		0.67
RBP_regulation_power_radar		2.0

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: rs740423; hg19: chr19-1978271; COSMIC: COSV55336483; COSMIC: COSV55336483;