rs6988353

Variant names:

• chr8-74085007-G-A
• rs6988353
• ENST00000519323.1:n.304-14412G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-74085007-G-A
• chr8-74085007-G-T

Variant summary

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

The ENST00000519323.1(ENSG00000254288):​n.304-14412G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0699 in 152,176 control chromosomes in the GnomAD database, including 844 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 0.070 (844 hom., cov: 32)
• Consequence: ENSG00000254288 ENST00000519323.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 2 publications found

Genes affected

ENSG00000254288 (HGNC:):

LY96 (HGNC:17156): (lymphocyte antigen 96) This gene encodes a protein which associates with toll-like receptor 4 on the cell surface and confers responsiveness to lipopolysaccyaride (LPS), thus providing a link between the receptor and LPS signaling. Studies of the mouse ortholog suggest that this gene may be involved in endotoxin neutralization. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LY96	XM_017013299.2	c.385-14412G>A		intron_variant	Intron 4 of 4		XP_016868788.1
LY96	XM_017013300.2	c.295-14412G>A		intron_variant	Intron 3 of 3		XP_016868789.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254288	ENST00000519323.1	n.304-14412G>A		intron_variant	Intron 1 of 1	1
ENSG00000254288	ENST00000756705.1	n.277-21660G>A		intron_variant	Intron 1 of 1
ENSG00000254288	ENST00000756706.1	n.405+11709G>A		intron_variant	Intron 2 of 2
ENSG00000254288	ENST00000756707.1	n.361-14412G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0698 AC: 10621 AN: 152058 Hom.: 842 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0365

Gnomad ASJ AF: 0.0138

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00725

Gnomad FIN AF: 0.0301

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0182

Gnomad OTH AF: 0.0602

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0699 AC: 10640 AN: 152176 Hom.: 844 Cov.: 32 AF XY: 0.0675 AC XY: 5022 AN XY: 74392

African (AFR) AF: 0.200 AC: 8306 AN: 41494

American (AMR) AF: 0.0364 AC: 556 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0138 AC: 48 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.00726 AC: 35 AN: 4822

European-Finnish (FIN) AF: 0.0301 AC: 319 AN: 10594

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0182 AC: 1235 AN: 68008

Other (OTH) AF: 0.0596 AC: 126 AN: 2114

Alfa AF: 0.0320 Hom.: 437

Bravo AF: 0.0773

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.71
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6988353; hg19: chr8-74997242;