chr12-10159690-G-A

Variant names:

• chr12-10159690-G-A
• rs1050283
• NM_002543.4:c.*190C>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.*190C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 493,990 control chromosomes in the GnomAD database, including 49,178 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 0.40 (13741 hom., cov: 32)
  • Exomes 𝑓: 0.44 (35437 hom.)
• Consequence: OLR1 NM_002543.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 25 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OLR1	NM_002543.4	c.*190C>T		3_prime_UTR_variant	Exon 6 of 6	ENST00000309539.8	NP_002534.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OLR1	ENST00000309539.8	c.*190C>T		3_prime_UTR_variant	Exon 6 of 6	1	NM_002543.4	ENSP00000309124.3

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61088 AN: 151928 Hom.: 13738 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.460

GnomAD4 exome AF: 0.440 AC: 150499 AN: 341944 Hom.: 35437 Cov.: 4 AF XY: 0.438 AC XY: 77748 AN XY: 177664

African (AFR) AF: 0.208 AC: 2333 AN: 11192

American (AMR) AF: 0.528 AC: 8910 AN: 16890

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 6245 AN: 10546

East Asian (EAS) AF: 0.205 AC: 5806 AN: 28390

South Asian (SAS) AF: 0.290 AC: 7048 AN: 24308

European-Finnish (FIN) AF: 0.489 AC: 10872 AN: 22236

Middle Eastern (MID) AF: 0.530 AC: 753 AN: 1422

European-Non Finnish (NFE) AF: 0.480 AC: 99409 AN: 206928

Other (OTH) AF: 0.455 AC: 9123 AN: 20032

GnomAD4 genome AF: 0.402 AC: 61100 AN: 152046 Hom.: 13741 Cov.: 32 AF XY: 0.402 AC XY: 29846 AN XY: 74336

African (AFR) AF: 0.208 AC: 8641 AN: 41456

American (AMR) AF: 0.522 AC: 7975 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1997 AN: 3472

East Asian (EAS) AF: 0.231 AC: 1196 AN: 5174

South Asian (SAS) AF: 0.287 AC: 1385 AN: 4826

European-Finnish (FIN) AF: 0.494 AC: 5206 AN: 10548

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33153 AN: 67962

Other (OTH) AF: 0.456 AC: 965 AN: 2116

Alfa AF: 0.491 Hom.: 8780

Bravo AF: 0.399

Asia WGS AF: 0.257 AC: 897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.28
PhyloP100		0.031
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: rs1050283; hg19: chr12-10312289; COSMIC: COSV58873016; COSMIC: COSV58873016;