Genetic Variant OLR1:c.565-73C>T (chr12-10160535-G-A) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_002543.4(OLR1):c.565-73C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 1,238,012 control chromosomes in the GnomAD database, including 129,541 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.40 ( 13741 hom., cov: 32)

Exomes 𝑓: 0.45 ( 115800 hom. )

Consequence

OLR1
NM_002543.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.512

Publications

18 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 -16 ACMG points.

BP6

Variant 12-10160535-G-A is Benign according to our data. Variant chr12-10160535-G-A is described in ClinVar as Benign. ClinVar VariationId is 1227465.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

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.565-73C>T	intron	N/A	NP_002534.1	P78380-1
OLR1	NM_001172633.2		c.564+251C>T	intron	N/A	NP_001166104.1	P78380-3
OLR1	NM_001172632.2		c.425-73C>T	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.565-73C>T	intron	N/A	ENSP00000309124.3	P78380-1
OLR1	ENST00000896632.1		c.565-85C>T	intron	N/A	ENSP00000566691.1
OLR1	ENST00000539518.5	TSL:2	c.406-73C>T	intron	N/A	ENSP00000442389.1	F5H7N8

Frequencies

GnomAD3 genomes

AF:

0.402

AC:

61079

AN:

151806

Hom.:

13738

Cov.:

show subpopulations

Gnomad AFR

AF:

0.209

Gnomad AMI

AF:

0.454

Gnomad AMR

AF:

0.521

Gnomad ASJ

AF:

0.576

Gnomad EAS

AF:

0.232

Gnomad SAS

AF:

0.286

Gnomad FIN

AF:

0.495

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.488

Gnomad OTH

AF:

0.461

GnomAD4 exome

AF:

0.452

AC:

490997

AN:

1086088

Hom.:

115800

Cov.:

AF XY:

0.449

AC XY:

247466

AN XY:

551160

show subpopulations

African (AFR)

AF:

0.201

AC:

5153

AN:

25664

American (AMR)

AF:

0.517

AC:

17597

AN:

34004

Ashkenazi Jewish (ASJ)

AF:

0.591

AC:

13067

AN:

22106

East Asian (EAS)

AF:

0.206

AC:

7537

AN:

36588

South Asian (SAS)

AF:

0.305

AC:

22701

AN:

74396

European-Finnish (FIN)

AF:

0.490

AC:

24752

AN:

50530

Middle Eastern (MID)

AF:

0.506

AC:

2531

AN:

5004

European-Non Finnish (NFE)

AF:

0.476

AC:

376267

AN:

790146

Other (OTH)

AF:

0.449

AC:

21392

AN:

47650

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

13126

26252

39379

52505

65631

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9546

19092

28638

38184

47730

<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:

61091

AN:

151924

Hom.:

13741

Cov.:

AF XY:

0.402

AC XY:

29835

AN XY:

74242

show subpopulations

African (AFR)

AF:

0.209

AC:

8646

AN:

41418

American (AMR)

AF:

0.521

AC:

7960

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.576

AC:

1996

AN:

3468

East Asian (EAS)

AF:

0.231

AC:

1199

AN:

5180

South Asian (SAS)

AF:

0.287

AC:

1380

AN:

4812

European-Finnish (FIN)

AF:

0.495

AC:

5210

AN:

10520

Middle Eastern (MID)

AF:

0.568

AC:

167

AN:

294

European-Non Finnish (NFE)

AF:

0.488

AC:

33158

AN:

67952

Other (OTH)

AF:

0.457

AC:

964

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1776

3552

5328

7104

8880

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

572

1144

1716

2288

2860

<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.:

8498

Bravo

AF:

0.399

Asia WGS

AF:

0.256

AC:

895

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

(source)

DANN

Benign

0.71

PhyloP100

0.51

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.29

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.29

Position offset: -20

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