chr12-10159363-T-G

Position:

• chr12-10159363-T-G

Variant summary

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

The ENST00000309539.8(OLR1):​c.*517A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 153,004 control chromosomes in the GnomAD database, including 13,877 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 (13743 hom., cov: 31)
  • Exomes 𝑓: 0.43 (134 hom.)
• Consequence: OLR1 ENST00000309539.8 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OLR1	NM_002543.4	c.*517A>C		3_prime_UTR_variant	6/6	ENST00000309539.8	NP_002534.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OLR1	ENST00000309539.8	c.*517A>C		3_prime_UTR_variant	6/6	1	NM_002543.4	ENSP00000309124	P1

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61046 AN: 151648 Hom.: 13740 Cov.: 31

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.461

GnomAD4 exome AF: 0.427 AC: 529 AN: 1238 Hom.: 134 Cov.: 0 AF XY: 0.426 AC XY: 287 AN XY: 674

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.431

Gnomad4 ASJ exome AF: 0.333

Gnomad4 EAS exome AF: 0.250

Gnomad4 SAS exome AF: 0.255

Gnomad4 FIN exome AF: 0.564

Gnomad4 NFE exome AF: 0.426

Gnomad4 OTH exome AF: 0.188

GnomAD4 genome AF: 0.402 AC: 61058 AN: 151766 Hom.: 13743 Cov.: 31 AF XY: 0.402 AC XY: 29798 AN XY: 74124

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.457

Alfa AF: 0.470 Hom.: 21110

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	-0.85
CADD	Benign	2.8
DANN	Benign	0.70

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: rs10505755; hg19: chr12-10311962;