Variant 6-31672202-C-T 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.526C>T(p.Arg176Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0683 in 1,612,998 control chromosomes in the GnomAD database, including 4,242 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 0.078 ( 513 hom., cov: 32)

Exomes 𝑓: 0.067 ( 3729 hom. )

Consequence

LY6G5B
NM_021221.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.584

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=0.0018301308).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.108 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.526C>T	p.Arg176Cys	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.526C>T	p.Arg176Cys	missense_variant	3/3	1	NM_021221.3	P1	Q8NDX9-1
LY6G5B	ENST00000409525.1 linkuse as main transcript	c.361C>T	p.Arg121Cys	missense_variant	2/2	1			Q8NDX9-2

Frequencies

GnomAD3 genomes

AF:

0.0782

AC:

11892

AN:

152090

Hom.:

514

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0939

Gnomad AMI

AF:

0.105

Gnomad AMR

AF:

0.0515

Gnomad ASJ

AF:

0.0589

Gnomad EAS

AF:

0.0718

Gnomad SAS

AF:

0.115

Gnomad FIN

AF:

0.0820

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.0724

Gnomad OTH

AF:

0.0773

GnomAD3 exomes

AF:

0.0738

AC:

18193

AN:

246644

Hom.:

785

AF XY:

0.0759

AC XY:

10203

AN XY:

134422

show subpopulations

Gnomad AFR exome

AF:

0.100

Gnomad AMR exome

AF:

0.0441

Gnomad ASJ exome

AF:

0.0600

Gnomad EAS exome

AF:

0.0907

Gnomad SAS exome

AF:

0.101

Gnomad FIN exome

AF:

0.0807

Gnomad NFE exome

AF:

0.0694

Gnomad OTH exome

AF:

0.0691

GnomAD4 exome

AF:

0.0673

AC:

98325

AN:

1460790

Hom.:

3729

Cov.:

AF XY:

0.0685

AC XY:

49781

AN XY:

726712

show subpopulations

Gnomad4 AFR exome

AF:

0.101

Gnomad4 AMR exome

AF:

0.0465

Gnomad4 ASJ exome

AF:

0.0595

Gnomad4 EAS exome

AF:

0.0436

Gnomad4 SAS exome

AF:

0.106

Gnomad4 FIN exome

AF:

0.0793

Gnomad4 NFE exome

AF:

0.0648

Gnomad4 OTH exome

AF:

0.0655

GnomAD4 genome

AF:

0.0781

AC:

11889

AN:

152208

Hom.:

513

Cov.:

AF XY:

0.0789

AC XY:

5872

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.0936

Gnomad4 AMR

AF:

0.0513

Gnomad4 ASJ

AF:

0.0589

Gnomad4 EAS

AF:

0.0723

Gnomad4 SAS

AF:

0.116

Gnomad4 FIN

AF:

0.0820

Gnomad4 NFE

AF:

0.0724

Gnomad4 OTH

AF:

0.0764

Alfa

AF:

0.0727

Hom.:

854

Bravo

AF:

0.0771

TwinsUK

AF:

0.0550

AC:

204

ALSPAC

AF:

0.0584

AC:

225

ESP6500AA

AF:

0.0956

AC:

289

ESP6500EA

AF:

0.0698

AC:

378

ExAC

AF:

0.0760

AC:

8980

Asia WGS

AF:

0.0760

AC:

264

AN:

3478

EpiCase

AF:

0.0716

EpiControl

AF:

0.0705

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.59

BayesDel_noAF

Benign

-0.54

CADD

Benign

DANN

Benign

0.95

DEOGEN2

Benign

0.26

.;.;T;.

Eigen

Benign

-0.25

Eigen_PC

Benign

-0.37

FATHMM_MKL

Benign

0.38

LIST_S2

Benign

0.71

T;T;T;T

MetaRNN

Benign

0.0018

T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.2

.;.;L;.

PROVEAN

Uncertain

-2.4

.;.;N;D

REVEL

Benign

0.059

Sift

Benign

0.11

.;.;T;T

Sift4G

Pathogenic

0.0

D;D;D;D

Polyphen

1.0

.;.;D;.

Vest4

0.13

MPC

0.16

ClinPred

0.024

GERP RS

2.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

Varity_R

0.10

gMVP

0.24

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