chr8-74007514-A-T

Variant names:

• chr8-74007514-A-T
• rs16938758
• NM_015364.5:c.203-2487A>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.203-2487A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,082 control chromosomes in the GnomAD database, including 5,785 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 (5785 hom., cov: 33)
• Consequence: LY96 NM_015364.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 9 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=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.437 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.203-2487A>T		intron	N/A	NP_056179.4	Q9Y6Y9-1
	LY96	NM_001195797.2		c.113-2487A>T		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.203-2487A>T		intron	N/A	ENSP00000284818.2	Q9Y6Y9-1
	LY96	ENST00000518893.1	TSL:3	c.113-2487A>T		intron	N/A	ENSP00000430533.1	Q9Y6Y9-2
	LY96	ENST00000962532.1		c.202+2629A>T		intron	N/A	ENSP00000632591.1

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37045 AN: 151964 Hom.: 5768 Cov.: 33

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.0963

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.244 AC: 37097 AN: 152082 Hom.: 5785 Cov.: 33 AF XY: 0.240 AC XY: 17815 AN XY: 74344

African (AFR) AF: 0.443 AC: 18347 AN: 41434

American (AMR) AF: 0.194 AC: 2972 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 680 AN: 3470

East Asian (EAS) AF: 0.0957 AC: 496 AN: 5182

South Asian (SAS) AF: 0.157 AC: 758 AN: 4828

European-Finnish (FIN) AF: 0.137 AC: 1445 AN: 10580

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11564 AN: 67978

Other (OTH) AF: 0.249 AC: 526 AN: 2114

Alfa AF: 0.0838 Hom.: 102

Bravo AF: 0.259

Asia WGS AF: 0.169 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	7.3
DANN	Benign	0.81
PhyloP100		0.14
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: rs16938758; hg19: chr8-74919749;