NM_021221.3:c.187+68G>A

Variant names:

• chr6-31671352-G-A
• rs2142234
• NM_021221.3:c.187+68G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 25 publications found

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]

ENSG00000263020 (HGNC:):

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021221.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY6G5B	NM_021221.3	MANE Select	c.187+68G>A		intron	N/A	NP_067044.2	A0A1U9X7Y3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY6G5B	ENST00000375864.5	TSL:1 MANE Select	c.187+68G>A		intron	N/A	ENSP00000365024.4	Q8NDX9-1
	ENSG00000263020	ENST00000617558.2	TSL:1	c.496+68G>A		intron	N/A	ENSP00000483989.2	N0E472
	ENSG00000263020	ENST00000375880.6	TSL:3	c.686+68G>A		intron	N/A	ENSP00000365040.2	Q5SRQ3

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

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

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

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: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0763 AC: 5188 AN: 67998

Other (OTH) AF: 0.0967 AC: 204 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.43
PhyloP100		-0.28
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2142234; hg19: chr6-31639129;