dbSNP rs17174597: OLR1:c.681-71A>G (chr12-10160092-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0140

Publications

7 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 -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 link	c.681-71A>G		intron_variant	Intron 5 of 5	ENST00000309539.8	NP_002534.1	P78380-1A0A024RAU0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OLR1	ENST00000309539.8 link	c.681-71A>G		intron_variant	Intron 5 of 5	1	NM_002543.4	ENSP00000309124.3		P78380-1

Frequencies

GnomAD3 genomes

AF:

0.402

AC:

61100

AN:

151972

Hom.:

13740

Cov.:

show subpopulations

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

show subpopulations

African (AFR)

AF:

0.196

AC:

5922

AN:

30226

American (AMR)

AF:

0.516

AC:

17054

AN:

33040

Ashkenazi Jewish (ASJ)

AF:

0.590

AC:

13370

AN:

22648

East Asian (EAS)

AF:

0.207

AC:

8026

AN:

38726

South Asian (SAS)

AF:

0.302

AC:

23104

AN:

76486

European-Finnish (FIN)

AF:

0.486

AC:

21810

AN:

44872

Middle Eastern (MID)

AF:

0.509

AC:

2723

AN:

5352

European-Non Finnish (NFE)

AF:

0.480

AC:

502327

AN:

1046460

Other (OTH)

AF:

0.450

AC:

25145

AN:

55910

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

15022

30044

45066

60088

75110

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14856

29712

44568

59424

74280

<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:

0.402

AC:

61112

AN:

152090

Hom.:

13743

Cov.:

AF XY:

0.401

AC XY:

29847

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.208

AC:

8650

AN:

41504

American (AMR)

AF:

0.522

AC:

7978

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.575

AC:

1997

AN:

3472

East Asian (EAS)

AF:

0.231

AC:

1197

AN:

5172

South Asian (SAS)

AF:

0.287

AC:

1384

AN:

4828

European-Finnish (FIN)

AF:

0.494

AC:

5209

AN:

10542

Middle Eastern (MID)

AF:

0.568

AC:

167

AN:

294

European-Non Finnish (NFE)

AF:

0.488

AC:

33155

AN:

67966

Other (OTH)

AF:

0.456

AC:

963

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1776

3553

5329

7106

8882

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

570

1140

1710

2280

2850

<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:

0.432

Hom.:

1963

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

(source)

DANN

Benign

0.82

PhyloP100

-0.014

Mutation Taster

=100/0

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over