rs13306593

Variant names:

• chr12-10160049-C-A
• rs13306593
• NM_002543.4:c.681-28G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-10160049-C-A
• chr12-10160049-C-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.681-28G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 1,572,126 control chromosomes in the GnomAD database, including 169,150 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 (13703 hom., cov: 32)
  • Exomes 𝑓: 0.46 (155447 hom.)
• Consequence: OLR1 NM_002543.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486
• Publications: 11 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.512 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.681-28G>T		intron	N/A	NP_002534.1	P78380-1
	OLR1	NM_001172633.2		c.565-28G>T		intron	N/A	NP_001166104.1	P78380-3
	OLR1	NM_001172632.2		c.541-28G>T		intron	N/A	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.681-28G>T		intron	N/A	ENSP00000309124.3	P78380-1
	OLR1	ENST00000896632.1		c.669-28G>T		intron	N/A	ENSP00000566691.1
	OLR1	ENST00000539518.5	TSL:2	c.522-28G>T		intron	N/A	ENSP00000442389.1	F5H7N8

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61012 AN: 151786 Hom.: 13700 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.571

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: 0.459

GnomAD2 exomes AF: 0.432 AC: 98568 AN: 228326 AF XY: 0.431

Gnomad AFR exome AF: 0.210

Gnomad AMR exome AF: 0.508

Gnomad ASJ exome AF: 0.587

Gnomad EAS exome AF: 0.234

Gnomad FIN exome AF: 0.490

Gnomad NFE exome AF: 0.484

Gnomad OTH exome AF: 0.478

GnomAD4 exome AF: 0.460 AC: 653560 AN: 1420224 Hom.: 155447 Cov.: 34 AF XY: 0.458 AC XY: 321329 AN XY: 702306

African (AFR) AF: 0.198 AC: 6276 AN: 31746

American (AMR) AF: 0.515 AC: 19392 AN: 37648

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 14390 AN: 24492

East Asian (EAS) AF: 0.208 AC: 8111 AN: 39034

South Asian (SAS) AF: 0.305 AC: 25042 AN: 82118

European-Finnish (FIN) AF: 0.489 AC: 24999 AN: 51088

Middle Eastern (MID) AF: 0.510 AC: 2840 AN: 5570

European-Non Finnish (NFE) AF: 0.483 AC: 526133 AN: 1090100

Other (OTH) AF: 0.451 AC: 26377 AN: 58428

GnomAD4 genome AF: 0.402 AC: 61023 AN: 151902 Hom.: 13703 Cov.: 32 AF XY: 0.401 AC XY: 29788 AN XY: 74230

African (AFR) AF: 0.209 AC: 8643 AN: 41446

American (AMR) AF: 0.522 AC: 7961 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1962 AN: 3438

East Asian (EAS) AF: 0.232 AC: 1198 AN: 5172

South Asian (SAS) AF: 0.287 AC: 1382 AN: 4820

European-Finnish (FIN) AF: 0.494 AC: 5208 AN: 10544

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

European-Non Finnish (NFE) AF: 0.488 AC: 33130 AN: 67920

Other (OTH) AF: 0.455 AC: 958 AN: 2106

Alfa AF: 0.432 Hom.: 2003

Bravo AF: 0.398

Asia WGS AF: 0.256 AC: 896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.33
DANN	Benign	0.22
PhyloP100		-0.49
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: rs13306593; hg19: chr12-10312648; COSMIC: COSV58873026; COSMIC: COSV58873026;