rs2277737

Positions:

• chr19-1978834-C-T

Variant summary

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

The NM_001319.7(CSNK1G2):​c.448-25C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0199 in 1,592,444 control chromosomes in the GnomAD database, including 428 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 0.017 (51 hom., cov: 31)
  • Exomes 𝑓: 0.020 (377 hom.)
• Consequence: CSNK1G2 NM_001319.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870

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=-0.85).
• BA1: GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSNK1G2	NM_001319.7	c.448-25C>T		intron_variant		ENST00000255641.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSNK1G2	ENST00000255641.13	c.448-25C>T		intron_variant		1	NM_001319.7	P1

Frequencies

GnomAD3 genomes AF: 0.0171 AC: 2585 AN: 151536 Hom.: 50 Cov.: 31

Gnomad AFR AF: 0.00748

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0352

Gnomad ASJ AF: 0.00519

Gnomad EAS AF: 0.0470

Gnomad SAS AF: 0.0220

Gnomad FIN AF: 0.0168

Gnomad MID AF: 0.00323

Gnomad NFE AF: 0.0172

Gnomad OTH AF: 0.0139

GnomAD3 exomes AF: 0.0275 AC: 6134 AN: 222906 Hom.: 134 AF XY: 0.0248 AC XY: 3067 AN XY: 123428

Gnomad AFR exome AF: 0.00710

Gnomad AMR exome AF: 0.0754

Gnomad ASJ exome AF: 0.00397

Gnomad EAS exome AF: 0.0431

Gnomad SAS exome AF: 0.0171

Gnomad FIN exome AF: 0.0204

Gnomad NFE exome AF: 0.0180

Gnomad OTH exome AF: 0.0273

GnomAD4 exome AF: 0.0202 AC: 29137 AN: 1440788 Hom.: 377 Cov.: 42 AF XY: 0.0199 AC XY: 14245 AN XY: 716006

Gnomad4 AFR exome AF: 0.00727

Gnomad4 AMR exome AF: 0.0697

Gnomad4 ASJ exome AF: 0.00431

Gnomad4 EAS exome AF: 0.0371

Gnomad4 SAS exome AF: 0.0186

Gnomad4 FIN exome AF: 0.0215

Gnomad4 NFE exome AF: 0.0187

Gnomad4 OTH exome AF: 0.0173

GnomAD4 genome AF: 0.0171 AC: 2590 AN: 151656 Hom.: 51 Cov.: 31 AF XY: 0.0177 AC XY: 1314 AN XY: 74104

Gnomad4 AFR AF: 0.00746

Gnomad4 AMR AF: 0.0354

Gnomad4 ASJ AF: 0.00519

Gnomad4 EAS AF: 0.0477

Gnomad4 SAS AF: 0.0216

Gnomad4 FIN AF: 0.0168

Gnomad4 NFE AF: 0.0172

Gnomad4 OTH AF: 0.0142

Alfa AF: 0.0153 Hom.: 6

Bravo AF: 0.0193

Asia WGS AF: 0.0270 AC: 95 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.80
DANN	Benign	0.58
RBP_binding_hub_radar		0.97
RBP_regulation_power_radar		2.3

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: rs2277737; hg19: chr19-1978833;