dbSNP rs10505755: OLR1:c.*517A>C (chr12-10159363-T-G) – 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.*517A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 153,004 control chromosomes in the GnomAD database, including 13,877 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: 31)

Exomes 𝑓: 0.43 ( 134 hom. )

Consequence

OLR1
NM_002543.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0830

Publications

11 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=-0.85).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OLR1	NM_002543.4 link	c.*517A>C		3_prime_UTR_variant	Exon 6 of 6	ENST00000309539.8	NP_002534.1	P78380-1A0A024RAU0

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
OLR1	ENST00000309539.8 link	c.*517A>C	3_prime_UTR_variant	Exon 6 of 6	1	NM_002543.4	ENSP00000309124.3	P78380-1
OLR1	ENST00000544577.5 link	c.*517A>C	downstream_gene_variant		5		ENSP00000444457.1	F5GZH1
OLR1	ENST00000543993.5 link	c.*653A>C	downstream_gene_variant		2		ENSP00000445085.1	B7ZAN8

Frequencies

GnomAD3 genomes

AF:

0.403

AC:

61046

AN:

151648

Hom.:

13740

Cov.:

show subpopulations

Gnomad AFR

AF:

0.209

Gnomad AMI

AF:

0.455

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:

0.461

GnomAD4 exome

AF:

0.427

AC:

529

AN:

1238

Hom.:

134

Cov.:

AF XY:

0.426

AC XY:

287

AN XY:

674

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AF:

0.431

AC:

AN:

202

Ashkenazi Jewish (ASJ)

AF:

0.333

AC:

AN:

East Asian (EAS)

AF:

0.250

AC:

AN:

South Asian (SAS)

AF:

0.255

AC:

AN:

102

European-Finnish (FIN)

AF:

0.564

AC:

114

AN:

202

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.426

AC:

289

AN:

678

Other (OTH)

AF:

0.188

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

61058

AN:

151766

Hom.:

13743

Cov.:

AF XY:

0.402

AC XY:

29798

AN XY:

74124

show subpopulations

African (AFR)

AF:

0.209

AC:

8634

AN:

41340

American (AMR)

AF:

0.522

AC:

7966

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.575

AC:

1996

AN:

3470

East Asian (EAS)

AF:

0.231

AC:

1191

AN:

5148

South Asian (SAS)

AF:

0.287

AC:

1378

AN:

4808

European-Finnish (FIN)

AF:

0.494

AC:

5182

AN:

10488

Middle Eastern (MID)

AF:

0.568

AC:

167

AN:

294

European-Non Finnish (NFE)

AF:

0.488

AC:

33170

AN:

67950

Other (OTH)

AF:

0.457

AC:

959

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1704

3407

5111

6814

8518

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:

0.460

Hom.:

29032

Bravo

AF:

0.399

Asia WGS

AF:

0.257

AC:

897

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.8

(source)

DANN

Benign

0.70

PhyloP100

0.083

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