5-149515312-T-C

Variant names:

• chr5-149515312-T-C
• rs10515629
• NM_001892.6:c.457-2103A>G

Variant summary

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

The NM_001892.6(CSNK1A1):​c.457-2103A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,136 control chromosomes in the GnomAD database, including 5,035 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 0.24 (5035 hom., cov: 32)
• Consequence: CSNK1A1 NM_001892.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• Publications: 2 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSNK1A1	NM_001892.6	c.457-2103A>G		intron_variant	Intron 4 of 9	ENST00000377843.8	NP_001883.4
CSNK1A1	NM_001025105.3	c.541-2103A>G		intron_variant	Intron 5 of 10		NP_001020276.1
CSNK1A1	NM_001271741.2	c.457-2103A>G		intron_variant	Intron 4 of 9		NP_001258670.1
CSNK1A1	NM_001271742.2	c.274-2103A>G		intron_variant	Intron 4 of 9		NP_001258671.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSNK1A1	ENST00000377843.8	c.457-2103A>G		intron_variant	Intron 4 of 9	1	NM_001892.6	ENSP00000367074.2

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36319 AN: 152018 Hom.: 5027 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.239 AC: 36338 AN: 152136 Hom.: 5035 Cov.: 32 AF XY: 0.244 AC XY: 18173 AN XY: 74372

African (AFR) AF: 0.128 AC: 5330 AN: 41556

American (AMR) AF: 0.400 AC: 6106 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 506 AN: 3466

East Asian (EAS) AF: 0.306 AC: 1583 AN: 5180

South Asian (SAS) AF: 0.393 AC: 1896 AN: 4824

European-Finnish (FIN) AF: 0.243 AC: 2569 AN: 10570

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17527 AN: 67946

Other (OTH) AF: 0.256 AC: 539 AN: 2108

Alfa AF: 0.258 Hom.: 3261

Bravo AF: 0.243

Asia WGS AF: 0.351 AC: 1218 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	12
DANN	Benign	0.84
PhyloP100		0.017
Mutation Taster		=100/0	polymorphism (auto)

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: rs10515629; hg19: chr5-148894875;