Variant chr6-31672068-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_021221.3(LY6G5B):c.392C>A(p.Ser131Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0288 in 1,613,012 control chromosomes in the GnomAD database, including 1,475 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.054 ( 407 hom., cov: 32)

Exomes 𝑓: 0.026 ( 1068 hom. )

Consequence

LY6G5B
NM_021221.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.116

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017583966).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LY6G5B	NM_021221.3 linkuse as main transcript	c.392C>A	p.Ser131Tyr	missense_variant	3/3	ENST00000375864.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LY6G5B	ENST00000375864.5 linkuse as main transcript	c.392C>A	p.Ser131Tyr	missense_variant	3/3	1	NM_021221.3	P1	Q8NDX9-1
LY6G5B	ENST00000409525.1 linkuse as main transcript	c.227C>A	p.Ser76Tyr	missense_variant	2/2	1			Q8NDX9-2

Frequencies

GnomAD3 genomes

AF:

0.0541

AC:

8223

AN:

152084

Hom.:

402

Cov.:

show subpopulations

Gnomad AFR

AF:

0.116

Gnomad AMI

AF:

0.00330

Gnomad AMR

AF:

0.0601

Gnomad ASJ

AF:

0.140

Gnomad EAS

AF:

0.0171

Gnomad SAS

AF:

0.0186

Gnomad FIN

AF:

0.00198

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0238

Gnomad OTH

AF:

0.0800

GnomAD3 exomes

AF:

0.0362

AC:

8925

AN:

246572

Hom.:

370

AF XY:

0.0328

AC XY:

4414

AN XY:

134386

show subpopulations

Gnomad AFR exome

AF:

0.119

Gnomad AMR exome

AF:

0.0564

Gnomad ASJ exome

AF:

0.143

Gnomad EAS exome

AF:

0.0134

Gnomad SAS exome

AF:

0.0168

Gnomad FIN exome

AF:

0.00268

Gnomad NFE exome

AF:

0.0239

Gnomad OTH exome

AF:

0.0506

GnomAD4 exome

AF:

0.0261

AC:

38183

AN:

1460810

Hom.:

1068

Cov.:

AF XY:

0.0258

AC XY:

18766

AN XY:

726722

show subpopulations

Gnomad4 AFR exome

AF:

0.117

Gnomad4 AMR exome

AF:

0.0580

Gnomad4 ASJ exome

AF:

0.141

Gnomad4 EAS exome

AF:

0.0449

Gnomad4 SAS exome

AF:

0.0174

Gnomad4 FIN exome

AF:

0.00283

Gnomad4 NFE exome

AF:

0.0195

Gnomad4 OTH exome

AF:

0.0404

GnomAD4 genome

AF:

0.0542

AC:

8250

AN:

152202

Hom.:

407

Cov.:

AF XY:

0.0521

AC XY:

3880

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.117

Gnomad4 AMR

AF:

0.0601

Gnomad4 ASJ

AF:

0.140

Gnomad4 EAS

AF:

0.0172

Gnomad4 SAS

AF:

0.0182

Gnomad4 FIN

AF:

0.00198

Gnomad4 NFE

AF:

0.0238

Gnomad4 OTH

AF:

0.0791

Alfa

AF:

0.0337

Hom.:

165

Bravo

AF:

0.0623

TwinsUK

AF:

0.0170

AC:

ALSPAC

AF:

0.0187

AC:

ESP6500AA

AF:

0.111

AC:

334

ESP6500EA

AF:

0.0281

AC:

152

ExAC

AF:

0.0343

AC:

4045

Asia WGS

AF:

0.0310

AC:

107

AN:

3478

EpiCase

AF:

0.0309

EpiControl

AF:

0.0331

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.61

CADD

Benign

DANN

Benign

0.74

DEOGEN2

Benign

0.077

.;.;T;.

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.16

LIST_S2

Benign

0.47

T;T;T;T

MetaRNN

Benign

0.0018

T;T;T;T

MetaSVM

Benign

-0.99

MutationAssessor

Benign

1.9

.;.;L;.

PROVEAN

Benign

-1.9

.;.;N;D

REVEL

Benign

0.014

Sift

Uncertain

0.026

.;.;D;D

Sift4G

Uncertain

0.0020

D;D;D;D

Polyphen

0.21

.;.;B;.

Vest4

0.11

MPC

0.18

ClinPred

0.0023

GERP RS

-0.40

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Varity_R

0.039

gMVP

0.15

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

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over