Genetic Variant OLR1:c.564+120G>A (chr12-10160666-C-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.564+120G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 1,332,176 control chromosomes in the GnomAD database, including 138,032 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 ( 13737 hom., cov: 32)

Exomes 𝑓: 0.45 ( 124295 hom. )

Consequence

OLR1
NM_002543.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.356

Publications

12 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:

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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=-0.88).

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
OLR1	NM_002543.4	MANE Select	c.564+120G>A	intron	N/A	NP_002534.1	P78380-1
OLR1	NM_001172633.2		c.564+120G>A	intron	N/A	NP_001166104.1	P78380-3
OLR1	NM_001172632.2		c.425-204G>A	intron	N/A	NP_001166103.1	P78380-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
OLR1	ENST00000309539.8	TSL:1 MANE Select	c.564+120G>A	intron	N/A	ENSP00000309124.3	P78380-1
OLR1	ENST00000896632.1		c.564+120G>A	intron	N/A	ENSP00000566691.1
OLR1	ENST00000539518.5	TSL:2	c.405+120G>A	intron	N/A	ENSP00000442389.1	F5H7N8

Frequencies

GnomAD3 genomes

AF:

0.402

AC:

61078

AN:

151900

Hom.:

13734

Cov.:

show subpopulations

Gnomad AFR

AF:

0.209

Gnomad AMI

AF:

0.458

Gnomad AMR

AF:

0.522

Gnomad ASJ

AF:

0.576

Gnomad EAS

AF:

0.230

Gnomad SAS

AF:

0.286

Gnomad FIN

AF:

0.494

Gnomad MID

AF:

0.561

Gnomad NFE

AF:

0.488

Gnomad OTH

AF:

0.460

GnomAD4 exome

AF:

0.450

AC:

531534

AN:

1180160

Hom.:

124295

Cov.:

AF XY:

0.448

AC XY:

264471

AN XY:

589758

show subpopulations

African (AFR)

AF:

0.196

AC:

5440

AN:

27698

American (AMR)

AF:

0.516

AC:

19576

AN:

37940

Ashkenazi Jewish (ASJ)

AF:

0.588

AC:

12107

AN:

20574

East Asian (EAS)

AF:

0.207

AC:

7883

AN:

38112

South Asian (SAS)

AF:

0.302

AC:

21217

AN:

70180

European-Finnish (FIN)

AF:

0.488

AC:

23726

AN:

48660

Middle Eastern (MID)

AF:

0.509

AC:

2352

AN:

4620

European-Non Finnish (NFE)

AF:

0.473

AC:

416752

AN:

881930

Other (OTH)

AF:

0.446

AC:

22481

AN:

50446

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

13570

27139

40709

54278

67848

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11446

22892

34338

45784

57230

<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:

61089

AN:

152016

Hom.:

13737

Cov.:

AF XY:

0.402

AC XY:

29852

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.208

AC:

8646

AN:

41480

American (AMR)

AF:

0.522

AC:

7960

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.576

AC:

1995

AN:

3466

East Asian (EAS)

AF:

0.230

AC:

1191

AN:

5182

South Asian (SAS)

AF:

0.287

AC:

1384

AN:

4826

European-Finnish (FIN)

AF:

0.494

AC:

5210

AN:

10548

Middle Eastern (MID)

AF:

0.572

AC:

167

AN:

292

European-Non Finnish (NFE)

AF:

0.488

AC:

33158

AN:

67944

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

1737

3474

5212

6949

8686

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:

0.453

Hom.:

8509

Bravo

AF:

0.399

Asia WGS

AF:

0.256

AC:

895

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

7.3

(source)

DANN

Benign

0.55

PhyloP100

-0.36

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.14

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