Variant rs3736235 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000309539.8(OLR1):c.565-14A>G variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 1,584,552 control chromosomes in the GnomAD database, including 171,160 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 ( 13734 hom., cov: 31)

Exomes 𝑓: 0.46 ( 157426 hom. )

Consequence

OLR1
ENST00000309539.8 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.97

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

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.565-14A>G		splice_polypyrimidine_tract_variant, 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.565-14A>G		splice_polypyrimidine_tract_variant, intron_variant		1	NM_002543.4	ENSP00000309124	P1	P78380-1

Frequencies

GnomAD3 genomes

AF:

0.402

AC:

61065

AN:

151820

Hom.:

13731

Cov.:

show subpopulations

Gnomad AFR

AF:

0.209

Gnomad AMI

AF:

0.455

Gnomad AMR

AF:

0.522

Gnomad ASJ

AF:

0.576

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:

0.460

GnomAD3 exomes

AF:

0.435

AC:

104299

AN:

239886

Hom.:

24028

AF XY:

0.434

AC XY:

56120

AN XY:

129424

show subpopulations

Gnomad AFR exome

AF:

0.211

Gnomad AMR exome

AF:

0.510

Gnomad ASJ exome

AF:

0.599

Gnomad EAS exome

AF:

0.236

Gnomad SAS exome

AF:

0.302

Gnomad FIN exome

AF:

0.489

Gnomad NFE exome

AF:

0.485

Gnomad OTH exome

AF:

0.486

GnomAD4 exome

AF:

0.461

AC:

660734

AN:

1432614

Hom.:

157426

Cov.:

AF XY:

0.459

AC XY:

327291

AN XY:

713658

show subpopulations

Gnomad4 AFR exome

AF:

0.201

Gnomad4 AMR exome

AF:

0.517

Gnomad4 ASJ exome

AF:

0.593

Gnomad4 EAS exome

AF:

0.208

Gnomad4 SAS exome

AF:

0.307

Gnomad4 FIN exome

AF:

0.490

Gnomad4 NFE exome

AF:

0.484

Gnomad4 OTH exome

AF:

0.453

GnomAD4 genome

AF:

0.402

AC:

61077

AN:

151938

Hom.:

13734

Cov.:

AF XY:

0.402

AC XY:

29828

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.208

Gnomad4 AMR

AF:

0.522

Gnomad4 ASJ

AF:

0.576

Gnomad4 EAS

AF:

0.232

Gnomad4 SAS

AF:

0.287

Gnomad4 FIN

AF:

0.494

Gnomad4 NFE

AF:

0.488

Gnomad4 OTH

AF:

0.456

Alfa

AF:

0.461

Hom.:

3742

Bravo

AF:

0.399

Asia WGS

AF:

0.256

AC:

895

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.0

DANN

Benign

0.56

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

Details are displayed if max score is > 0.2

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over