NM_002543.4:c.179-888C>T

Variant names:

• chr12-10167845-G-A
• rs3741860
• NM_002543.4:c.179-888C>T

Variant summary

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

The NM_002543.4(OLR1):​c.179-888C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 151,794 control chromosomes in the GnomAD database, including 33,571 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 0.66 (33571 hom., cov: 30)
• Consequence: OLR1 NM_002543.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 13 publications found

Genes affected

OLR1 (HGNC:8133): (oxidized low density lipoprotein receptor 1) This gene encodes a low density lipoprotein receptor that belongs to the C-type lectin superfamily. This gene is regulated through the cyclic AMP signaling pathway. The encoded protein binds, internalizes and degrades oxidized low-density lipoprotein. This protein may be involved in the regulation of Fas-induced apoptosis. This protein may play a role as a scavenger receptor. Mutations of this gene have been associated with atherosclerosis, risk of myocardial infarction, and may modify the risk of Alzheimer's disease. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Feb 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OLR1	NM_002543.4	c.179-888C>T		intron_variant	Intron 2 of 5	ENST00000309539.8	NP_002534.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OLR1	ENST00000309539.8	c.179-888C>T		intron_variant	Intron 2 of 5	1	NM_002543.4	ENSP00000309124.3

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99607 AN: 151678 Hom.: 33547 Cov.: 30

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.657 AC: 99680 AN: 151794 Hom.: 33571 Cov.: 30 AF XY: 0.654 AC XY: 48480 AN XY: 74142

African (AFR) AF: 0.540 AC: 22316 AN: 41318

American (AMR) AF: 0.688 AC: 10488 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2704 AN: 3470

East Asian (EAS) AF: 0.399 AC: 2065 AN: 5170

South Asian (SAS) AF: 0.593 AC: 2857 AN: 4814

European-Finnish (FIN) AF: 0.674 AC: 7079 AN: 10502

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.734 AC: 49921 AN: 67970

Other (OTH) AF: 0.685 AC: 1439 AN: 2100

Alfa AF: 0.699 Hom.: 21406

Bravo AF: 0.653

Asia WGS AF: 0.501 AC: 1746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.3
DANN	Benign	0.79
PhyloP100		-0.12
PromoterAI		-0.038	Neutral
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: rs3741860; hg19: chr12-10320444;