rs7001413

Variant names:

• chr8-74097998-G-T
• rs7001413
• ENST00000519323.1:n.304-1421G>T

Variant summary

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

The ENST00000519323.1(ENSG00000254288):​n.304-1421G>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: ENSG00000254288 ENST00000519323.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 4 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=-0.91).
• 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 rank	MANE	Protein	UniProt
LY96	XM_017013299.2	c.385-1421G>T		intron_variant	Intron 4 of 4		XP_016868788.1
LY96	XM_017013300.2	c.295-1421G>T		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.304-1421G>T		intron_variant	Intron 1 of 1	1
ENSG00000254288	ENST00000668834.2	n.193+4279G>T		intron_variant	Intron 1 of 2
ENSG00000254288	ENST00000756705.1	n.277-8669G>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.130 AC: 5385 AN: 41484

American (AMR) AF: 0.0423 AC: 647 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0409 AC: 142 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.00768 AC: 37 AN: 4818

European-Finnish (FIN) AF: 0.0375 AC: 398 AN: 10614

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0239 AC: 1628 AN: 68000

Other (OTH) AF: 0.0643 AC: 136 AN: 2116

Alfa AF: 0.0357 Hom.: 257

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
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs7001413; hg19: chr8-75010233;