NM_015364.5:c.332-3325C>T

Variant names:

• chr8-74023464-C-T
• rs7838017
• NM_015364.5:c.332-3325C>T

Variant summary

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

The NM_015364.5(LY96):​c.332-3325C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,098 control chromosomes in the GnomAD database, including 5,233 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 0.24 (5233 hom., cov: 32)
• Consequence: LY96 NM_015364.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520
• Publications: 4 publications found

Genes affected

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 = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LY96	NM_015364.5	c.332-3325C>T		intron_variant	Intron 3 of 4	ENST00000284818.7	NP_056179.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LY96	ENST00000284818.7	c.332-3325C>T		intron_variant	Intron 3 of 4	1	NM_015364.5	ENSP00000284818.2
LY96	ENST00000518893.1	c.242-3325C>T		intron_variant	Intron 2 of 3	3		ENSP00000430533.1

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36867 AN: 151980 Hom.: 5211 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.243 AC: 36939 AN: 152098 Hom.: 5233 Cov.: 32 AF XY: 0.241 AC XY: 17917 AN XY: 74366

African (AFR) AF: 0.392 AC: 16243 AN: 41466

American (AMR) AF: 0.260 AC: 3976 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 867 AN: 3466

East Asian (EAS) AF: 0.120 AC: 622 AN: 5162

South Asian (SAS) AF: 0.172 AC: 827 AN: 4816

European-Finnish (FIN) AF: 0.180 AC: 1906 AN: 10584

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.173 AC: 11757 AN: 67998

Other (OTH) AF: 0.239 AC: 505 AN: 2116

Alfa AF: 0.220 Hom.: 572

Bravo AF: 0.258

Asia WGS AF: 0.190 AC: 661 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	3.1
DANN	Benign	0.53
PhyloP100		0.052
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: rs7838017; hg19: chr8-74935699;