rs9328374

Variant names:

• chr6-6591396-G-A
• rs9328374
• NM_004271.4:c.136+2526G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004271.4(LY86):​c.136+2526G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 153,710 control chromosomes in the GnomAD database, including 40,585 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 0.72 (40114 hom., cov: 32)
  • Exomes 𝑓: 0.76 (471 hom.)
• Consequence: LY86 NM_004271.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280
• Publications: 13 publications found

Genes affected

LY86 (HGNC:16837): (lymphocyte antigen 86) Acts upstream of or within positive regulation of lipopolysaccharide-mediated signaling pathway. Predicted to be located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

LY86-AS1 (HGNC:26593): (LY86 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LY86	NM_004271.4	c.136+2526G>A		intron_variant	Intron 1 of 4	ENST00000230568.5	NP_004262.1
LY86-AS1	NR_026970.1	n.196-21907C>T		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LY86	ENST00000230568.5	c.136+2526G>A		intron_variant	Intron 1 of 4	1	NM_004271.4	ENSP00000230568.3

Frequencies

GnomAD3 genomes AF: 0.724 AC: 110018 AN: 151944 Hom.: 40099 Cov.: 32

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.717

GnomAD4 exome AF: 0.757 AC: 1247 AN: 1648 Hom.: 471 Cov.: 0 AF XY: 0.757 AC XY: 666 AN XY: 880

African (AFR) AF: 0.750 AC: 3 AN: 4

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.755 AC: 1164 AN: 1542

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.792 AC: 57 AN: 72

Other (OTH) AF: 0.750 AC: 18 AN: 24

GnomAD4 genome AF: 0.724 AC: 110066 AN: 152062 Hom.: 40114 Cov.: 32 AF XY: 0.722 AC XY: 53651 AN XY: 74332

African (AFR) AF: 0.628 AC: 26039 AN: 41454

American (AMR) AF: 0.731 AC: 11172 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2734 AN: 3470

East Asian (EAS) AF: 0.658 AC: 3404 AN: 5172

South Asian (SAS) AF: 0.742 AC: 3568 AN: 4810

European-Finnish (FIN) AF: 0.763 AC: 8068 AN: 10570

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.775 AC: 52702 AN: 67982

Other (OTH) AF: 0.712 AC: 1505 AN: 2114

Alfa AF: 0.756 Hom.: 24114

Bravo AF: 0.720

Asia WGS AF: 0.651 AC: 2267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.6
DANN	Benign	0.51
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs9328374; hg19: chr6-6591629;