Genetic Variant NM_020896.4:c.840C>T (chr11-3107797-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_020896.4(OSBPL5):c.840C>T(p.Thr280Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 1,611,992 control chromosomes in the GnomAD database, including 162,251 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 0.50 ( 20749 hom., cov: 32)

Exomes 𝑓: 0.43 ( 141502 hom. )

Consequence

OSBPL5
NM_020896.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.07

Publications

15 publications found

Variant links:

Genes affected

OSBPL5 (HGNC:16392): (oxysterol binding protein like 5) This gene encodes a member of the oxysterol-binding protein (OSBP) family, a group of intracellular lipid receptors that play a key role in the maintenance of cholesterol balance in the body. Most members contain an N-terminal pleckstrin homology domain and a highly conserved C-terminal OSBP-like sterol-binding domain. This gene has been shown to be imprinted, with preferential expression from the maternal allele only in placenta. Transcript variants encoding different isoforms have been identified. [provided by RefSeq, Oct 2010]

OSBPL5 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP7

Synonymous conserved (PhyloP=1.07 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL5	NM_020896.4 link	c.840C>T	p.Thr280Thr	synonymous_variant	Exon 8 of 22	ENST00000263650.12	NP_065947.1	Q9H0X9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSBPL5	ENST00000263650.12 link	c.840C>T	p.Thr280Thr	synonymous_variant	Exon 8 of 22	1	NM_020896.4	ENSP00000263650.7		Q9H0X9-1

Frequencies

GnomAD3 genomes

AF:

0.497

AC:

75399

AN:

151846

Hom.:

20707

Cov.:

show subpopulations

Gnomad AFR

AF:

0.723

Gnomad AMI

AF:

0.447

Gnomad AMR

AF:

0.427

Gnomad ASJ

AF:

0.455

Gnomad EAS

AF:

0.0509

Gnomad SAS

AF:

0.479

Gnomad FIN

AF:

0.386

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.430

Gnomad OTH

AF:

0.475

GnomAD2 exomes

AF:

0.409

AC:

101557

AN:

248518

AF XY:

0.412

show subpopulations

Gnomad AFR exome

AF:

0.737

Gnomad AMR exome

AF:

0.327

Gnomad ASJ exome

AF:

0.457

Gnomad EAS exome

AF:

0.0394

Gnomad FIN exome

AF:

0.375

Gnomad NFE exome

AF:

0.428

Gnomad OTH exome

AF:

0.415

GnomAD4 exome

AF:

0.432

AC:

630326

AN:

1460026

Hom.:

141502

Cov.:

AF XY:

0.432

AC XY:

313598

AN XY:

726366

show subpopulations

African (AFR)

AF:

0.734

AC:

24573

AN:

33478

American (AMR)

AF:

0.335

AC:

14974

AN:

44696

Ashkenazi Jewish (ASJ)

AF:

0.447

AC:

11684

AN:

26134

East Asian (EAS)

AF:

0.0686

AC:

2725

AN:

39700

South Asian (SAS)

AF:

0.479

AC:

41352

AN:

86252

European-Finnish (FIN)

AF:

0.377

AC:

19488

AN:

51722

Middle Eastern (MID)

AF:

0.411

AC:

2369

AN:

5766

European-Non Finnish (NFE)

AF:

0.438

AC:

487365

AN:

1111892

Other (OTH)

AF:

0.427

AC:

25796

AN:

60386

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

22302

44604

66905

89207

111509

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14802

29604

44406

59208

74010

<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:

0.497

AC:

75501

AN:

151966

Hom.:

20749

Cov.:

AF XY:

0.490

AC XY:

36401

AN XY:

74250

show subpopulations

African (AFR)

AF:

0.723

AC:

29991

AN:

41466

American (AMR)

AF:

0.426

AC:

6509

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.455

AC:

1580

AN:

3472

East Asian (EAS)

AF:

0.0508

AC:

261

AN:

5138

South Asian (SAS)

AF:

0.480

AC:

2313

AN:

4816

European-Finnish (FIN)

AF:

0.386

AC:

4085

AN:

10576

Middle Eastern (MID)

AF:

0.422

AC:

124

AN:

294

European-Non Finnish (NFE)

AF:

0.430

AC:

29235

AN:

67916

Other (OTH)

AF:

0.473

AC:

997

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1768

3536

5303

7071

8839

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

646

1292

1938

2584

3230

<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:

0.461

Hom.:

12764

Bravo

AF:

0.504

Asia WGS

AF:

0.295

AC:

1025

AN:

3478

EpiCase

AF:

0.440

EpiControl

AF:

0.436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

8.1

(source)

DANN

Benign

0.66

PhyloP100

1.1

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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