Variant rs2242653 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001003693.3(LY6G6F):c.500G>A(p.Arg167Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 1,612,924 control chromosomes in the GnomAD database, including 20,791 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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 0.15 ( 2073 hom., cov: 32)

Exomes 𝑓: 0.15 ( 18718 hom. )

Consequence

LY6G6F
NM_001003693.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.723

Variant links:

Genes affected

LY6G6F (HGNC:13933): (lymphocyte antigen 6 family member G6F) The human G6f protein is a type I transmembrane protein belonging to the immunoglobin (Ig) superfamily, which is comprised of cell-surface proteins involved in the immune system and cellular recognition (de Vet et al., 2003 [PubMed 12852788]).[supplied by OMIM, Mar 2008]

LY6G6F links:

LY6G6F-LY6G6D (HGNC:):

LY6G6F-LY6G6D 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=0.0023539662).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LY6G6F	NM_001003693.3 linkuse as main transcript	c.500G>A	p.Arg167Lys	missense_variant	3/6	ENST00000375832.5
LY6G6F-LY6G6D	NM_001353334.2 linkuse as main transcript	c.500G>A	p.Arg167Lys	missense_variant	3/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LY6G6F	ENST00000375832.5 linkuse as main transcript	c.500G>A	p.Arg167Lys	missense_variant	3/6	1	NM_001003693.3	P1	Q5SQ64-1

Frequencies

GnomAD3 genomes

AF:

0.153

AC:

23193

AN:

152056

Hom.:

2068

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0996

Gnomad AMI

AF:

0.149

Gnomad AMR

AF:

0.201

Gnomad ASJ

AF:

0.0409

Gnomad EAS

AF:

0.154

Gnomad SAS

AF:

0.151

Gnomad FIN

AF:

0.333

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.153

Gnomad OTH

AF:

0.122

GnomAD3 exomes

AF:

0.169

AC:

41685

AN:

246648

Hom.:

4177

AF XY:

0.164

AC XY:

22031

AN XY:

134408

show subpopulations

Gnomad AFR exome

AF:

0.0994

Gnomad AMR exome

AF:

0.243

Gnomad ASJ exome

AF:

0.0395

Gnomad EAS exome

AF:

0.146

Gnomad SAS exome

AF:

0.144

Gnomad FIN exome

AF:

0.317

Gnomad NFE exome

AF:

0.150

Gnomad OTH exome

AF:

0.155

GnomAD4 exome

AF:

0.152

AC:

222593

AN:

1460750

Hom.:

18718

Cov.:

AF XY:

0.151

AC XY:

109734

AN XY:

726686

show subpopulations

Gnomad4 AFR exome

AF:

0.0866

Gnomad4 AMR exome

AF:

0.234

Gnomad4 ASJ exome

AF:

0.0413

Gnomad4 EAS exome

AF:

0.219

Gnomad4 SAS exome

AF:

0.145

Gnomad4 FIN exome

AF:

0.315

Gnomad4 NFE exome

AF:

0.145

Gnomad4 OTH exome

AF:

0.139

GnomAD4 genome

AF:

0.153

AC:

23219

AN:

152174

Hom.:

2073

Cov.:

AF XY:

0.161

AC XY:

11949

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.0996

Gnomad4 AMR

AF:

0.202

Gnomad4 ASJ

AF:

0.0409

Gnomad4 EAS

AF:

0.154

Gnomad4 SAS

AF:

0.150

Gnomad4 FIN

AF:

0.333

Gnomad4 NFE

AF:

0.153

Gnomad4 OTH

AF:

0.122

Alfa

AF:

0.143

Hom.:

3434

Bravo

AF:

0.141

TwinsUK

AF:

0.141

AC:

523

ALSPAC

AF:

0.136

AC:

526

ESP6500AA

AF:

0.100

AC:

303

ESP6500EA

AF:

0.152

AC:

823

ExAC

AF:

0.163

AC:

19389

Asia WGS

AF:

0.176

AC:

610

AN:

3478

EpiCase

AF:

0.132

EpiControl

AF:

0.134

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.071

BayesDel_addAF

Benign

-0.81

BayesDel_noAF

Benign

-0.80

CADD

Benign

5.7

DANN

Benign

0.74

DEOGEN2

Benign

0.0038

T;.

Eigen

Benign

-1.1

Eigen_PC

Benign

-0.92

FATHMM_MKL

Benign

0.15

LIST_S2

Benign

0.45

T;.

MetaRNN

Benign

0.0024

T;T

MetaSVM

Benign

-0.91

MutationAssessor

Benign

1.3

L;.

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.37

PROVEAN

Benign

-0.18

N;N

REVEL

Benign

0.051

Sift

Benign

0.86

T;T

Sift4G

Benign

1.0

T;T

Polyphen

0.0020

B;.

Vest4

0.038

MPC

0.074

ClinPred

0.0014

GERP RS

0.87

Varity_R

0.038

gMVP

0.19

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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