12-10160849-C-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_002543.4(OLR1):c.501G>C(p.Lys167Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 1,613,828 control chromosomes in the GnomAD database, including 10,148 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign,risk factor (no stars).

Frequency

Genomes: 𝑓 0.13 ( 1541 hom., cov: 32)

Exomes 𝑓: 0.099 ( 8607 hom. )

Consequence

OLR1
NM_002543.4 missense

Scores

Clinical Significance

Benign; risk factor no assertion criteria provided B:1O:1

Conservation

PhyloP100: -0.0190

Publications

88 publications found

Variant links:

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]

OLR1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.001839906).

BP6

Variant 12-10160849-C-G is Benign according to our data. Variant chr12-10160849-C-G is described in ClinVar as Benign|risk_factor. ClinVar VariationId is 6994.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 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

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
OLR1	NM_002543.4	MANE Select	c.501G>C	p.Lys167Asn	missense	Exon 4 of 6	NP_002534.1	P78380-1
OLR1	NM_001172633.2		c.501G>C	p.Lys167Asn	missense	Exon 4 of 5	NP_001166104.1	P78380-3
OLR1	NM_001172632.2		c.425-387G>C		intron	N/A	NP_001166103.1	P78380-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
OLR1	ENST00000309539.8	TSL:1 MANE Select	c.501G>C	p.Lys167Asn	missense	Exon 4 of 6	ENSP00000309124.3	P78380-1
OLR1	ENST00000896632.1		c.501G>C	p.Lys167Asn	missense	Exon 4 of 6	ENSP00000566691.1
OLR1	ENST00000539518.5	TSL:2	c.342G>C	p.Lys114Asn	missense	Exon 3 of 5	ENSP00000442389.1	F5H7N8

Frequencies

GnomAD3 genomes

AF:

0.126

AC:

19128

AN:

152050

Hom.:

1539

Cov.:

show subpopulations

Gnomad AFR

AF:

0.218

Gnomad AMI

AF:

0.0746

Gnomad AMR

AF:

0.0606

Gnomad ASJ

AF:

0.0493

Gnomad EAS

AF:

0.170

Gnomad SAS

AF:

0.212

Gnomad FIN

AF:

0.0797

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0872

Gnomad OTH

AF:

0.110

GnomAD2 exomes

AF:

0.108

AC:

27102

AN:

251394

AF XY:

0.111

show subpopulations

Gnomad AFR exome

AF:

0.213

Gnomad AMR exome

AF:

0.0373

Gnomad ASJ exome

AF:

0.0469

Gnomad EAS exome

AF:

0.171

Gnomad FIN exome

AF:

0.0833

Gnomad NFE exome

AF:

0.0904

Gnomad OTH exome

AF:

0.0843

GnomAD4 exome

AF:

0.0993

AC:

145143

AN:

1461660

Hom.:

8607

Cov.:

AF XY:

0.101

AC XY:

73649

AN XY:

727132

show subpopulations

African (AFR)

AF:

0.214

AC:

7153

AN:

33474

American (AMR)

AF:

0.0396

AC:

1772

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.0449

AC:

1173

AN:

26132

East Asian (EAS)

AF:

0.192

AC:

7625

AN:

39694

South Asian (SAS)

AF:

0.199

AC:

17154

AN:

86214

European-Finnish (FIN)

AF:

0.0862

AC:

4603

AN:

53418

Middle Eastern (MID)

AF:

0.0661

AC:

381

AN:

5768

European-Non Finnish (NFE)

AF:

0.0892

AC:

99168

AN:

1111850

Other (OTH)

AF:

0.101

AC:

6114

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

6328

12656

18985

25313

31641

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3844

7688

11532

15376

19220

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.126

AC:

19149

AN:

152168

Hom.:

1541

Cov.:

AF XY:

0.125

AC XY:

9333

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.218

AC:

9061

AN:

41488

American (AMR)

AF:

0.0604

AC:

924

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0493

AC:

171

AN:

3472

East Asian (EAS)

AF:

0.170

AC:

881

AN:

5178

South Asian (SAS)

AF:

0.212

AC:

1023

AN:

4832

European-Finnish (FIN)

AF:

0.0797

AC:

843

AN:

10578

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0872

AC:

5930

AN:

68018

Other (OTH)

AF:

0.111

AC:

233

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

833

1666

2500

3333

4166

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

206

412

618

824

1030

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0921

Hom.:

572

Bravo

AF:

0.127

TwinsUK

AF:

0.0917

AC:

340

ALSPAC

AF:

0.0820

AC:

316

ESP6500AA

AF:

0.209

AC:

919

ESP6500EA

AF:

0.0908

AC:

781

ExAC

AF:

0.115

AC:

13967

Asia WGS

AF:

0.190

AC:

658

AN:

3478

EpiCase

AF:

0.0797

EpiControl

AF:

0.0844

ClinVar

ClinVar submissions

Significance:Benign; risk factor

Revision:no assertion criteria provided

View on ClinVar

Pathogenic

VUS

Benign

Condition

OLR1-related disorder (1)

Myocardial infarction, susceptibility to (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.32

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.65

CADD

Benign

(source)

DANN

Benign

0.63

DEOGEN2

Benign

0.064

Eigen

Benign

-0.65

Eigen_PC

Benign

-0.67

FATHMM_MKL

Benign

0.42

LIST_S2

Benign

0.74

MetaRNN

Benign

0.0018

MetaSVM

Benign

-0.94

MutationAssessor

Benign

1.5

PhyloP100

-0.019

PrimateAI

Benign

0.43

PROVEAN

Benign

-0.78

REVEL

Benign

0.035

Sift

Benign

0.12

Sift4G

Benign

0.28

Polyphen

0.63

Vest4

0.28

MutPred

0.23

Loss of ubiquitination at K167 (P = 0.0059)

MPC

0.37

ClinPred

0.015

GERP RS

-0.21

Varity_R

0.38

gMVP

0.38

Mutation Taster

=91/9

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over