Variant chr6-31670030-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1

The NM_021221.3(LY6G5B):c.-921C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 897,250 control chromosomes in the GnomAD database, including 42,643 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.37 ( 11200 hom., cov: 33)

Exomes 𝑓: 0.28 ( 31443 hom. )

Consequence

LY6G5B
NM_021221.3 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.55

Variant links:

Genes affected

LY6G5B (HGNC:13931): (lymphocyte antigen 6 family member G5B) LY6G5B belongs to a cluster of leukocyte antigen-6 (LY6) genes located in the major histocompatibility complex (MHC) class III region on chromosome 6. Members of the LY6 superfamily typically contain 70 to 80 amino acids, including 8 to 10 cysteines. Most LY6 proteins are attached to the cell surface by a glycosylphosphatidylinositol (GPI) anchor that is directly involved in signal transduction (Mallya et al., 2002 [PubMed 12079290]).[supplied by OMIM, Mar 2008]

LY6G5B links:

CSNK2B (HGNC:2460): (casein kinase 2 beta) This gene encodes the beta subunit of casein kinase II, a ubiquitous protein kinase which regulates metabolic pathways, signal transduction, transcription, translation, and replication. The enzyme is composed of three subunits, alpha, alpha prime and beta, which form a tetrameric holoenzyme. The alpha and alpha prime subunits are catalytic, while the beta subunit serves regulatory functions. The enzyme localizes to the endoplasmic reticulum and the Golgi apparatus. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]

CSNK2B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.33).

BP6

Variant 6-31670030-C-T is Benign according to our data. Variant chr6-31670030-C-T is described in ClinVar as [Benign]. Clinvar id is 1253018.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
LY6G5B	NM_021221.3 linkuse as main transcript	c.-921C>T	5_prime_UTR_variant	1/3	ENST00000375864.5	NP_067044.2
CSNK2B	NM_001320.7 linkuse as main transcript	c.*104C>T	3_prime_UTR_variant	7/7	ENST00000375882.7	NP_001311.3
CSNK2B	NM_001282385.2 linkuse as main transcript	c.*104C>T	3_prime_UTR_variant	7/7		NP_001269314.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LY6G5B	ENST00000375864.5 linkuse as main transcript	c.-921C>T		5_prime_UTR_variant	1/3	1	NM_021221.3	ENSP00000365024	P1	Q8NDX9-1
CSNK2B	ENST00000375882.7 linkuse as main transcript	c.*104C>T		3_prime_UTR_variant	7/7	1	NM_001320.7	ENSP00000365042	P1

Frequencies

GnomAD3 genomes

AF:

0.368

AC:

55883

AN:

151944

Hom.:

11188

Cov.:

show subpopulations

Gnomad AFR

AF:

0.526

Gnomad AMI

AF:

0.261

Gnomad AMR

AF:

0.389

Gnomad ASJ

AF:

0.297

Gnomad EAS

AF:

0.384

Gnomad SAS

AF:

0.310

Gnomad FIN

AF:

0.420

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.266

Gnomad OTH

AF:

0.374

GnomAD4 exome

AF:

0.281

AC:

209349

AN:

745188

Hom.:

31443

Cov.:

AF XY:

0.279

AC XY:

105739

AN XY:

379516

show subpopulations

Gnomad4 AFR exome

AF:

0.536

Gnomad4 AMR exome

AF:

0.397

Gnomad4 ASJ exome

AF:

0.302

Gnomad4 EAS exome

AF:

0.412

Gnomad4 SAS exome

AF:

0.288

Gnomad4 FIN exome

AF:

0.400

Gnomad4 NFE exome

AF:

0.251

Gnomad4 OTH exome

AF:

0.301

GnomAD4 genome

AF:

0.368

AC:

55937

AN:

152062

Hom.:

11200

Cov.:

AF XY:

0.375

AC XY:

27848

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.526

Gnomad4 AMR

AF:

0.390

Gnomad4 ASJ

AF:

0.297

Gnomad4 EAS

AF:

0.384

Gnomad4 SAS

AF:

0.310

Gnomad4 FIN

AF:

0.420

Gnomad4 NFE

AF:

0.266

Gnomad4 OTH

AF:

0.373

Alfa

AF:

0.284

Hom.:

8133

Bravo

AF:

0.376

Asia WGS

AF:

0.354

AC:

1228

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 11, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.33

CADD

Benign

DANN

Benign

0.92

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over