Genetic Variant NM_002543.4:c.564+27G>C (chr12-10160759-C-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.564+27G>C 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 1,607,182 control chromosomes in the GnomAD database, including 173,421 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 ( 13731 hom., cov: 32)

Exomes 𝑓: 0.46 ( 159690 hom. )

Consequence

OLR1
NM_002543.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.475

Publications

15 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.513 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.564+27G>C	intron	N/A	NP_002534.1	P78380-1
OLR1	NM_001172633.2		c.564+27G>C	intron	N/A	NP_001166104.1	P78380-3
OLR1	NM_001172632.2		c.425-297G>C	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.564+27G>C	intron	N/A	ENSP00000309124.3	P78380-1
OLR1	ENST00000896632.1		c.564+27G>C	intron	N/A	ENSP00000566691.1
OLR1	ENST00000539518.5	TSL:2	c.405+27G>C	intron	N/A	ENSP00000442389.1	F5H7N8

Frequencies

GnomAD3 genomes

AF:

0.402

AC:

61057

AN:

151868

Hom.:

13728

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:

0.230

Gnomad SAS

AF:

0.286

Gnomad FIN

AF:

0.493

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.488

Gnomad OTH

AF:

0.461

GnomAD2 exomes

AF:

0.434

AC:

108646

AN:

250530

AF XY:

0.433

show subpopulations

Gnomad AFR exome

AF:

0.209

Gnomad AMR exome

AF:

0.508

Gnomad ASJ exome

AF:

0.597

Gnomad EAS exome

AF:

0.234

Gnomad FIN exome

AF:

0.490

Gnomad NFE exome

AF:

0.483

Gnomad OTH exome

AF:

0.483

GnomAD4 exome

AF:

0.461

AC:

670326

AN:

1455196

Hom.:

159690

Cov.:

AF XY:

0.458

AC XY:

331049

AN XY:

722756

show subpopulations

African (AFR)

AF:

0.200

AC:

6669

AN:

33364

American (AMR)

AF:

0.516

AC:

22987

AN:

44564

Ashkenazi Jewish (ASJ)

AF:

0.592

AC:

15429

AN:

26052

East Asian (EAS)

AF:

0.208

AC:

8235

AN:

39514

South Asian (SAS)

AF:

0.307

AC:

26384

AN:

85998

European-Finnish (FIN)

AF:

0.490

AC:

26159

AN:

53338

Middle Eastern (MID)

AF:

0.513

AC:

2949

AN:

5748

European-Non Finnish (NFE)

AF:

0.483

AC:

534307

AN:

1106500

Other (OTH)

AF:

0.453

AC:

27207

AN:

60118

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

16092

32184

48275

64367

80459

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15564

31128

46692

62256

77820

<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:

61069

AN:

151986

Hom.:

13731

Cov.:

AF XY:

0.401

AC XY:

29823

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.208

AC:

8648

AN:

41482

American (AMR)

AF:

0.522

AC:

7967

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.576

AC:

1996

AN:

3468

East Asian (EAS)

AF:

0.230

AC:

1192

AN:

5178

South Asian (SAS)

AF:

0.287

AC:

1384

AN:

4820

European-Finnish (FIN)

AF:

0.493

AC:

5203

AN:

10544

Middle Eastern (MID)

AF:

0.568

AC:

167

AN:

294

European-Non Finnish (NFE)

AF:

0.488

AC:

33135

AN:

67928

Other (OTH)

AF:

0.457

AC:

962

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1732

3464

5197

6929

8661

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

570

1140

1710

2280

2850

<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:

0.467

Hom.:

3201

Bravo

AF:

0.399

Asia WGS

AF:

0.256

AC:

895

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.1

(source)

DANN

Benign

0.39

PhyloP100

-0.47

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over