Variant rs3736234 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The ENST00000309539.8(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
ENST00000309539.8 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.512

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 made for transcript

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OLR1	NM_002543.4 linkuse as main transcript	c.565-73C>T		intron_variant		ENST00000309539.8	NP_002534.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OLR1	ENST00000309539.8 linkuse as main transcript	c.565-73C>T		intron_variant		1	NM_002543.4	ENSP00000309124	P1	P78380-1

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

Gnomad4 AFR exome

AF:

0.201

Gnomad4 AMR exome

AF:

0.517

Gnomad4 ASJ exome

AF:

0.591

Gnomad4 EAS exome

AF:

0.206

Gnomad4 SAS exome

AF:

0.305

Gnomad4 FIN exome

AF:

0.490

Gnomad4 NFE exome

AF:

0.476

Gnomad4 OTH exome

AF:

0.449

GnomAD4 genome

AF:

0.402

AC:

61091

AN:

151924

Hom.:

13741

Cov.:

AF XY:

0.402

AC XY:

29835

AN XY:

74242

show subpopulations

Gnomad4 AFR

AF:

0.209

Gnomad4 AMR

AF:

0.521

Gnomad4 ASJ

AF:

0.576

Gnomad4 EAS

AF:

0.231

Gnomad4 SAS

AF:

0.287

Gnomad4 FIN

AF:

0.495

Gnomad4 NFE

AF:

0.488

Gnomad4 OTH

AF:

0.457

Alfa

AF:

0.454

Hom.:

7607

Bravo

AF:

0.399

Asia WGS

AF:

0.256

AC:

895

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 24, 2021	This variant is associated with the following publications: (PMID: 25904137) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

DANN

Benign

0.71

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over