rs17174597

Variant names:

• chr12-10160092-T-C
• rs17174597
• NM_002543.4:c.681-71A>G

Variant summary

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

The NM_002543.4(OLR1):​c.681-71A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 1,505,810 control chromosomes in the GnomAD database, including 160,697 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: 33)
  • Exomes 𝑓: 0.46 (146954 hom.)
• Consequence: OLR1 NM_002543.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

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=-0.83).
• 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.681-71A>G		intron_variant	Intron 5 of 5	ENST00000309539.8	NP_002534.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OLR1	ENST00000309539.8	c.681-71A>G		intron_variant	Intron 5 of 5	1	NM_002543.4	ENSP00000309124.3

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61100 AN: 151972 Hom.: 13740 Cov.: 33

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.454

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: 0.460

GnomAD4 exome AF: 0.458 AC: 619481 AN: 1353720 Hom.: 146954 AF XY: 0.455 AC XY: 304901 AN XY: 669602

Gnomad4 AFR exome AF: 0.196

Gnomad4 AMR exome AF: 0.516

Gnomad4 ASJ exome AF: 0.590

Gnomad4 EAS exome AF: 0.207

Gnomad4 SAS exome AF: 0.302

Gnomad4 FIN exome AF: 0.486

Gnomad4 NFE exome AF: 0.480

Gnomad4 OTH exome AF: 0.450

GnomAD4 genome AF: 0.402 AC: 61112 AN: 152090 Hom.: 13743 Cov.: 33 AF XY: 0.401 AC XY: 29847 AN XY: 74350

Gnomad4 AFR AF: 0.208

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: 0.456

Alfa AF: 0.441 Hom.: 1944

Bravo AF: 0.399

Asia WGS AF: 0.256 AC: 895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.6
DANN	Benign	0.82

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: rs17174597; hg19: chr12-10312691;