dbSNP rs2142234: LY6G5B:c.187+68G>A (chr6-31671352-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_021221.3(LY6G5B):c.187+68G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0755 in 1,604,086 control chromosomes in the GnomAD database, including 5,413 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 0.099 ( 896 hom., cov: 32)

Exomes 𝑓: 0.073 ( 4517 hom. )

Consequence

LY6G5B
NM_021221.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.277

Publications

25 publications found

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:

ENSG00000263020 (HGNC:):

ENSG00000263020 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LY6G5B	NM_021221.3 link	c.187+68G>A		intron_variant	Intron 2 of 2	ENST00000375864.5	NP_067044.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LY6G5B	ENST00000375864.5 link	c.187+68G>A		intron_variant	Intron 2 of 2	1	NM_021221.3	ENSP00000365024.4		Q8NDX9-1
ENSG00000263020	ENST00000375880.6 link	c.686+68G>A		intron_variant	Intron 7 of 7	3		ENSP00000365040.2		Q5SRQ3

Frequencies

GnomAD3 genomes

AF:

0.0991

AC:

15066

AN:

151984

Hom.:

898

Cov.:

show subpopulations

Gnomad AFR

AF:

0.154

Gnomad AMI

AF:

0.105

Gnomad AMR

AF:

0.0669

Gnomad ASJ

AF:

0.0749

Gnomad EAS

AF:

0.0785

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.0824

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.0763

Gnomad OTH

AF:

0.0977

GnomAD4 exome

AF:

0.0730

AC:

105963

AN:

1451984

Hom.:

4517

AF XY:

0.0742

AC XY:

53614

AN XY:

722550

show subpopulations

African (AFR)

AF:

0.164

AC:

5494

AN:

33402

American (AMR)

AF:

0.0564

AC:

2517

AN:

44650

Ashkenazi Jewish (ASJ)

AF:

0.0787

AC:

2046

AN:

26004

East Asian (EAS)

AF:

0.0465

AC:

1843

AN:

39672

South Asian (SAS)

AF:

0.115

AC:

9863

AN:

86116

European-Finnish (FIN)

AF:

0.0790

AC:

3746

AN:

47418

Middle Eastern (MID)

AF:

0.0862

AC:

474

AN:

5496

European-Non Finnish (NFE)

AF:

0.0680

AC:

75396

AN:

1109022

Other (OTH)

AF:

0.0761

AC:

4584

AN:

60204

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

5126

10251

15377

20502

25628

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2778

5556

8334

11112

13890

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0991

AC:

15067

AN:

152102

Hom.:

896

Cov.:

AF XY:

0.0992

AC XY:

7378

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.154

AC:

6382

AN:

41462

American (AMR)

AF:

0.0667

AC:

1019

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0749

AC:

260

AN:

3472

East Asian (EAS)

AF:

0.0790

AC:

409

AN:

5176

South Asian (SAS)

AF:

0.123

AC:

593

AN:

4810

European-Finnish (FIN)

AF:

0.0824

AC:

873

AN:

10592

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0763

AC:

5188

AN:

67998

Other (OTH)

AF:

0.0967

AC:

204

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

683

1367

2050

2734

3417

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

168

336

504

672

840

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0819

Hom.:

2024

Bravo

AF:

0.101

Asia WGS

AF:

0.0880

AC:

306

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.2

(source)

DANN

Benign

0.43

PhyloP100

-0.28

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over