rs13306593
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002543.4(OLR1):c.681-28G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 1,572,126 control chromosomes in the GnomAD database, including 169,150 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 ( 13703 hom., cov: 32)
Exomes 𝑓: 0.46 ( 155447 hom. )
Consequence
OLR1
NM_002543.4 intron
NM_002543.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.486
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]
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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=-0.97).
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 | UniProt |
---|---|---|---|---|---|---|---|
OLR1 | NM_002543.4 | c.681-28G>T | intron_variant | ENST00000309539.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OLR1 | ENST00000309539.8 | c.681-28G>T | intron_variant | 1 | NM_002543.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.402 AC: 61012AN: 151786Hom.: 13700 Cov.: 32
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GnomAD3 exomes AF: 0.432 AC: 98568AN: 228326Hom.: 22731 AF XY: 0.431 AC XY: 53717AN XY: 124542
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GnomAD4 exome AF: 0.460 AC: 653560AN: 1420224Hom.: 155447 Cov.: 34 AF XY: 0.458 AC XY: 321329AN XY: 702306
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GnomAD4 genome ? AF: 0.402 AC: 61023AN: 151902Hom.: 13703 Cov.: 32 AF XY: 0.401 AC XY: 29788AN XY: 74230
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at