rs12316150

chr12-10159692-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002543.4(OLR1):c.*188T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0833 in 494,736 control chromosomes in the GnomAD database, including 2,059 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 0.073 (521 hom., cov: 33)
  • Exomes 𝑓: 0.088 (1538 hom.)
• Consequence: OLR1 NM_002543.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OLR1	NM_002543.4	c.*188T>A		3_prime_UTR_variant	6/6	ENST00000309539.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OLR1	ENST00000309539.8	c.*188T>A		3_prime_UTR_variant	6/6	1	NM_002543.4	P1

Frequencies

GnomAD3 genomes AF: 0.0733 AC: 11159 AN: 152172 Hom.: 520 Cov.: 33

Gnomad AFR AF: 0.0315

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0646

Gnomad ASJ AF: 0.0975

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0606

Gnomad FIN AF: 0.0640

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0746

GnomAD4 exome AF: 0.0878 AC: 30053 AN: 342446 Hom.: 1538 Cov.: 5 AF XY: 0.0879 AC XY: 15643 AN XY: 177894

Gnomad4 AFR exome AF: 0.0291

Gnomad4 AMR exome AF: 0.0576

Gnomad4 ASJ exome AF: 0.102

Gnomad4 EAS exome AF: 0.000315

Gnomad4 SAS exome AF: 0.0618

Gnomad4 FIN exome AF: 0.0691

Gnomad4 NFE exome AF: 0.110

Gnomad4 OTH exome AF: 0.0887

GnomAD4 genome AF: 0.0733 AC: 11156 AN: 152290 Hom.: 521 Cov.: 33 AF XY: 0.0707 AC XY: 5268 AN XY: 74480

Gnomad4 AFR AF: 0.0315

Gnomad4 AMR AF: 0.0646

Gnomad4 ASJ AF: 0.0975

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.0608

Gnomad4 FIN AF: 0.0640

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.0733

Alfa AF: 0.0904 Hom.: 94

Bravo AF: 0.0712

Asia WGS AF: 0.0330 AC: 114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	3.5
Dann	Benign	0.48

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

Publications

LitVar

Other links and lift over

dbSNP: rs12316150; hg19: chr12-10312291;