rs1035549

Positions:

• chr16-58175841-C-T

Variant summary

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

The NM_001896.4(CSNK2A2):​c.370-1331G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,022 control chromosomes in the GnomAD database, including 7,282 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 0.30 (7282 hom., cov: 32)
• Consequence: CSNK2A2 NM_001896.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

Genes affected

CSNK2A2 (HGNC:2459): (casein kinase 2 alpha 2) This gene encodes the alpha', or alpha 2, catalytic subunit of the protein kinase enzyme, casein kinase 2 (CK2). Casein kinase 2 is a serine/threonine protein kinase that phosphorylates acidic proteins such as casein. It is involved in various cellular processes, including cell cycle control, apoptosis, and circadian rhythms. This heterotetrameric kinase includes two catalytic subunits, either alpha or alpha', and two regulatory beta subunits. The closely related gene paralog encoding the alpha, or alpha 1 subunit (CSNK2A1, Gene ID: 1457) is found on chromosome 20. An intronic variant in this gene (alpha 2) may be associated with leukocyte telomere length in a South Asian population. A related transcribed pseudogene is found on chromosome 11. [provided by RefSeq, Aug 2017]

CSNK2A2 (HGNC:):

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 = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSNK2A2	NM_001896.4	c.370-1331G>A		intron_variant		ENST00000262506.8	NP_001887.1
CSNK2A2	XM_047433626.1	c.370-1331G>A		intron_variant			XP_047289582.1
CSNK2A2	XM_005255801.4	c.-42-1331G>A		intron_variant			XP_005255858.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSNK2A2	ENST00000262506.8	c.370-1331G>A		intron_variant		1	NM_001896.4	ENSP00000262506.3

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45971 AN: 151904 Hom.: 7264 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.271

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.303 AC: 46030 AN: 152022 Hom.: 7282 Cov.: 32 AF XY: 0.307 AC XY: 22835 AN XY: 74280

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.274

Alfa AF: 0.248 Hom.: 8110

Bravo AF: 0.307

Asia WGS AF: 0.325 AC: 1128 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	3.5
DANN	Benign	0.42

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: rs1035549; hg19: chr16-58209745;