rs7001413

Positions:

• chr8-74097998-G-T

Variant summary

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

The XM_017013299.2(LY96):​c.385-1421G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0551 in 152,170 control chromosomes in the GnomAD database, including 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 0.055 (413 hom., cov: 32)
• Consequence: LY96 XM_017013299.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LY96	XM_017013299.2	c.385-1421G>T		intron_variant			XP_016868788.1
LY96	XM_017013300.2	c.295-1421G>T		intron_variant			XP_016868789.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000254288	ENST00000519323.1	n.304-1421G>T		intron_variant		1
ENSG00000253983	ENST00000668834.1	n.175+4279G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0549 AC: 8347 AN: 152052 Hom.: 405 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0425

Gnomad ASJ AF: 0.0409

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00767

Gnomad FIN AF: 0.0375

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0239

Gnomad OTH AF: 0.0602

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

GnomAD4 genome AF: 0.0551 AC: 8384 AN: 152170 Hom.: 413 Cov.: 32 AF XY: 0.0532 AC XY: 3957 AN XY: 74402

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.0423

Gnomad4 ASJ AF: 0.0409

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00768

Gnomad4 FIN AF: 0.0375

Gnomad4 NFE AF: 0.0239

Gnomad4 OTH AF: 0.0643

Alfa AF: 0.0309 Hom.: 105

Bravo AF: 0.0588

Asia WGS AF: 0.0290 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7001413; hg19: chr8-75010233;