rs10808798

Variant names:

• chr8-73994279-T-C
• rs10808798
• NM_015364.5:c.112+2725T>C

Your query was ambiguous. Multiple possible variants found:

• chr8-73994279-T-C
• chr8-73994279-T-G

Variant summary

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

The NM_015364.5(LY96):​c.112+2725T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 151,970 control chromosomes in the GnomAD database, including 16,829 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 0.47 (16829 hom., cov: 32)
• Consequence: LY96 NM_015364.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392
• Publications: 5 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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015364.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY96	NM_015364.5	MANE Select	c.112+2725T>C		intron	N/A	NP_056179.4	Q9Y6Y9-1
	LY96	NM_001195797.2		c.112+2725T>C		intron	N/A	NP_001182726.1	Q9Y6Y9-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LY96	ENST00000284818.7	TSL:1 MANE Select	c.112+2725T>C		intron	N/A	ENSP00000284818.2	Q9Y6Y9-1
	LY96	ENST00000518893.1	TSL:3	c.112+2725T>C		intron	N/A	ENSP00000430533.1	Q9Y6Y9-2
	LY96	ENST00000962532.1		c.112+2725T>C		intron	N/A	ENSP00000632591.1

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71325 AN: 151850 Hom.: 16799 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.470 AC: 71397 AN: 151970 Hom.: 16829 Cov.: 32 AF XY: 0.472 AC XY: 35025 AN XY: 74252

African (AFR) AF: 0.497 AC: 20603 AN: 41454

American (AMR) AF: 0.511 AC: 7795 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1421 AN: 3472

East Asian (EAS) AF: 0.315 AC: 1626 AN: 5166

South Asian (SAS) AF: 0.521 AC: 2508 AN: 4818

European-Finnish (FIN) AF: 0.474 AC: 4988 AN: 10534

Middle Eastern (MID) AF: 0.462 AC: 133 AN: 288

European-Non Finnish (NFE) AF: 0.453 AC: 30816 AN: 67964

Other (OTH) AF: 0.456 AC: 961 AN: 2108

Alfa AF: 0.455 Hom.: 4584

Bravo AF: 0.473

Asia WGS AF: 0.458 AC: 1591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.75
PhyloP100		-0.39
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: rs10808798; hg19: chr8-74906514;