dbSNP rs12316150: OLR1:c.*188T>A (chr12-10159692-A-T) – 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.*188T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0833 in 494,736 control chromosomes in the GnomAD database, including 2,059 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 0.073 ( 521 hom., cov: 33)

Exomes 𝑓: 0.088 ( 1538 hom. )

Consequence

OLR1
NM_002543.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.71

Publications

5 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=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OLR1	NM_002543.4 link	c.*188T>A		3_prime_UTR_variant	Exon 6 of 6	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.*188T>A		3_prime_UTR_variant	Exon 6 of 6	1	NM_002543.4	ENSP00000309124.3		P78380-1

Frequencies

GnomAD3 genomes

AF:

0.0733

AC:

11159

AN:

152172

Hom.:

520

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0315

Gnomad AMI

AF:

0.0395

Gnomad AMR

AF:

0.0646

Gnomad ASJ

AF:

0.0975

Gnomad EAS

AF:

0.00173

Gnomad SAS

AF:

0.0606

Gnomad FIN

AF:

0.0640

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.107

Gnomad OTH

AF:

0.0746

GnomAD4 exome

AF:

0.0878

AC:

30053

AN:

342446

Hom.:

1538

Cov.:

AF XY:

0.0879

AC XY:

15643

AN XY:

177894

show subpopulations

African (AFR)

AF:

0.0291

AC:

326

AN:

11216

American (AMR)

AF:

0.0576

AC:

977

AN:

16954

Ashkenazi Jewish (ASJ)

AF:

0.102

AC:

1076

AN:

10532

East Asian (EAS)

AF:

0.000315

AC:

AN:

28576

South Asian (SAS)

AF:

0.0618

AC:

1498

AN:

24250

European-Finnish (FIN)

AF:

0.0691

AC:

1553

AN:

22468

Middle Eastern (MID)

AF:

0.102

AC:

146

AN:

1438

European-Non Finnish (NFE)

AF:

0.110

AC:

22701

AN:

207090

Other (OTH)

AF:

0.0887

AC:

1767

AN:

19922

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1253

2506

3759

5012

6265

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

160

320

480

640

800

<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:

0.0733

AC:

11156

AN:

152290

Hom.:

521

Cov.:

AF XY:

0.0707

AC XY:

5268

AN XY:

74480

show subpopulations

African (AFR)

AF:

0.0315

AC:

1307

AN:

41548

American (AMR)

AF:

0.0646

AC:

988

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0975

AC:

338

AN:

3468

East Asian (EAS)

AF:

0.00173

AC:

AN:

5190

South Asian (SAS)

AF:

0.0608

AC:

294

AN:

4834

European-Finnish (FIN)

AF:

0.0640

AC:

679

AN:

10606

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.108

AC:

7313

AN:

68020

Other (OTH)

AF:

0.0733

AC:

155

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

533

1067

1600

2134

2667

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

136

272

408

544

680

<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:

0.0904

Hom.:

Bravo

AF:

0.0712

Asia WGS

AF:

0.0330

AC:

114

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.5

(source)

DANN

Benign

0.48

PhyloP100

1.7

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