chr8-74028651-A-T

Variant names:

• chr8-74028651-A-T
• rs2114169
• NM_015364.5:c.385-305A>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.385-305A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,020 control chromosomes in the GnomAD database, including 9,329 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 0.30 (9329 hom., cov: 32)
• Consequence: LY96 NM_015364.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• 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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LY96	NM_015364.5	c.385-305A>T		intron_variant	Intron 4 of 4	ENST00000284818.7	NP_056179.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LY96	ENST00000284818.7	c.385-305A>T		intron_variant	Intron 4 of 4	1	NM_015364.5	ENSP00000284818.2
LY96	ENST00000518893.1	c.295-305A>T		intron_variant	Intron 3 of 3	3		ENSP00000430533.1

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45455 AN: 151902 Hom.: 9288 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.300 AC: 45555 AN: 152020 Hom.: 9329 Cov.: 32 AF XY: 0.295 AC XY: 21955 AN XY: 74300

African (AFR) AF: 0.586 AC: 24273 AN: 41412

American (AMR) AF: 0.286 AC: 4375 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 887 AN: 3468

East Asian (EAS) AF: 0.121 AC: 625 AN: 5186

South Asian (SAS) AF: 0.172 AC: 829 AN: 4820

European-Finnish (FIN) AF: 0.181 AC: 1910 AN: 10556

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11816 AN: 67990

Other (OTH) AF: 0.283 AC: 595 AN: 2104

Alfa AF: 0.257 Hom.: 904

Bravo AF: 0.323

Asia WGS AF: 0.208 AC: 720 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.8
DANN	Benign	0.85
PhyloP100		-0.011
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: rs2114169; hg19: chr8-74940886;