rs2142234

Positions:

• chr6-31671352-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LY6G5B	NM_021221.3	c.187+68G>A		intron_variant		ENST00000375864.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LY6G5B	ENST00000375864.5	c.187+68G>A		intron_variant		1	NM_021221.3	P1
LY6G5B	ENST00000409525.1	c.22+68G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0991 AC: 15066 AN: 151984 Hom.: 898 Cov.: 32

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

Gnomad4 AFR exome AF: 0.164

Gnomad4 AMR exome AF: 0.0564

Gnomad4 ASJ exome AF: 0.0787

Gnomad4 EAS exome AF: 0.0465

Gnomad4 SAS exome AF: 0.115

Gnomad4 FIN exome AF: 0.0790

Gnomad4 NFE exome AF: 0.0680

Gnomad4 OTH exome AF: 0.0761

GnomAD4 genome AF: 0.0991 AC: 15067 AN: 152102 Hom.: 896 Cov.: 32 AF XY: 0.0992 AC XY: 7378 AN XY: 74350

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.0667

Gnomad4 ASJ AF: 0.0749

Gnomad4 EAS AF: 0.0790

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0824

Gnomad4 NFE AF: 0.0763

Gnomad4 OTH AF: 0.0967

Alfa AF: 0.0802 Hom.: 728

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
DANN	Benign	0.43

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

Other links and lift over

dbSNP: rs2142234; hg19: chr6-31639129;