rs12316150

Variant names:

• chr12-10159692-A-T
• rs12316150
• NM_002543.4:c.*188T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002543.4. 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
	OLR1	NM_002543.4	MANE Select	c.*188T>A		3_prime_UTR	Exon 6 of 6	NP_002534.1	P78380-1
	OLR1	NM_001172633.2		c.*324T>A		3_prime_UTR	Exon 5 of 5	NP_001166104.1	P78380-3
	OLR1	NM_001172632.2		c.*324T>A		3_prime_UTR	Exon 5 of 5	NP_001166103.1	P78380-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OLR1	ENST00000309539.8	TSL:1 MANE Select	c.*188T>A		3_prime_UTR	Exon 6 of 6	ENSP00000309124.3	P78380-1
	OLR1	ENST00000896632.1		c.*188T>A		3_prime_UTR	Exon 6 of 6	ENSP00000566691.1
	OLR1	ENST00000545927.5	TSL:2	c.*324T>A		3_prime_UTR	Exon 5 of 5	ENSP00000439251.1	P78380-3

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

African (AFR) AF: 0.0291 AC: 326 AN: 11216

American (AMR) AF: 0.0576 AC: 977 AN: 16954

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 1076 AN: 10532

East Asian (EAS) AF: 0.000315 AC: 9 AN: 28576

South Asian (SAS) AF: 0.0618 AC: 1498 AN: 24250

European-Finnish (FIN) AF: 0.0691 AC: 1553 AN: 22468

Middle Eastern (MID) AF: 0.102 AC: 146 AN: 1438

European-Non Finnish (NFE) AF: 0.110 AC: 22701 AN: 207090

Other (OTH) AF: 0.0887 AC: 1767 AN: 19922

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

African (AFR) AF: 0.0315 AC: 1307 AN: 41548

American (AMR) AF: 0.0646 AC: 988 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0975 AC: 338 AN: 3468

East Asian (EAS) AF: 0.00173 AC: 9 AN: 5190

South Asian (SAS) AF: 0.0608 AC: 294 AN: 4834

European-Finnish (FIN) AF: 0.0640 AC: 679 AN: 10606

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7313 AN: 68020

Other (OTH) AF: 0.0733 AC: 155 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.5
DANN	Benign	0.48
PhyloP100		1.7
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: rs12316150; hg19: chr12-10312291;