chr5-149505809-A-T

Position:

• chr5-149505809-A-T

Variant summary

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

The NM_001892.6(CSNK1A1):​c.858-214T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,104 control chromosomes in the GnomAD database, including 5,318 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 0.25 (5318 hom., cov: 32)
• Consequence: CSNK1A1 NM_001892.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.65

Genes affected

CSNK1A1 (HGNC:2451): (casein kinase 1 alpha 1) Enables protein serine/threonine kinase activity. Involved in several processes, including negative regulation of canonical Wnt signaling pathway; peptidyl-serine phosphorylation; and positive regulation of proteasomal ubiquitin-dependent protein catabolic process. Located in centrosome; cytosol; and nuclear speck. Part of beta-catenin destruction complex. Colocalizes with keratin filament and mRNA cleavage and polyadenylation specificity factor complex. Biomarker of Alzheimer's disease and inclusion body myositis. [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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSNK1A1	NM_001892.6	c.858-214T>A		intron_variant		ENST00000377843.8
CSNK1A1	NM_001025105.3	c.942-214T>A		intron_variant
CSNK1A1	NM_001271741.2	c.858-214T>A		intron_variant
CSNK1A1	NM_001271742.2	c.675-214T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSNK1A1	ENST00000377843.8	c.858-214T>A		intron_variant		1	NM_001892.6	A1

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38088 AN: 151986 Hom.: 5310 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.251 AC: 38124 AN: 152104 Hom.: 5318 Cov.: 32 AF XY: 0.256 AC XY: 19036 AN XY: 74356

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.263

Alfa AF: 0.255 Hom.: 672

Bravo AF: 0.256

Asia WGS AF: 0.356 AC: 1237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.3
DANN	Benign	0.56

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: rs3733847; hg19: chr5-148885372;