19-1981031-C-T

Variant names:

• chr19-1981031-C-T
• rs4806825
• NM_001319.7:c.*828C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001319.7(CSNK1G2):​c.*828C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.021 in 152,220 control chromosomes in the GnomAD database, including 57 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 0.021 (57 hom., cov: 33)
  • Exomes 𝑓: 0.011 (0 hom.)
• Consequence: CSNK1G2 NM_001319.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0557 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001319.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSNK1G2	NM_001319.7	MANE Select	c.*828C>T		3_prime_UTR	Exon 12 of 12	NP_001310.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSNK1G2	ENST00000255641.13	TSL:1 MANE Select	c.*828C>T		3_prime_UTR	Exon 12 of 12	ENSP00000255641.7	P78368
	CSNK1G2	ENST00000890346.1		c.*828C>T		3_prime_UTR	Exon 12 of 12	ENSP00000560405.1
	CSNK1G2	ENST00000890347.1		c.*828C>T		3_prime_UTR	Exon 13 of 13	ENSP00000560406.1

Frequencies

GnomAD3 genomes AF: 0.0210 AC: 3194 AN: 152012 Hom.: 56 Cov.: 33

Gnomad AFR AF: 0.0306

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0587

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.00310

Gnomad FIN AF: 0.00141

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0115

Gnomad OTH AF: 0.0230

GnomAD4 exome AF: 0.0111 AC: 1 AN: 90 Hom.: 0 Cov.: 0 AF XY: 0.0147 AC XY: 1 AN XY: 68

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0139 AC: 1 AN: 72

Other (OTH) AF: 0.00 AC: 0 AN: 6

GnomAD4 genome AF: 0.0210 AC: 3201 AN: 152130 Hom.: 57 Cov.: 33 AF XY: 0.0210 AC XY: 1560 AN XY: 74384

African (AFR) AF: 0.0306 AC: 1267 AN: 41390

American (AMR) AF: 0.0589 AC: 901 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3472

East Asian (EAS) AF: 0.0216 AC: 112 AN: 5178

South Asian (SAS) AF: 0.00310 AC: 15 AN: 4832

European-Finnish (FIN) AF: 0.00141 AC: 15 AN: 10624

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0115 AC: 784 AN: 68018

Other (OTH) AF: 0.0223 AC: 47 AN: 2110

Alfa AF: 0.0157 Hom.: 6

Bravo AF: 0.0273

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.85
PhyloP100		-0.088
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs4806825; hg19: chr19-1981030;