Genetic Variant OSBPL10:p.Pro603Pro (chr3-31670901-C-T) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_017784.5(OSBPL10):c.1809G>A(p.Pro603Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 1,613,690 control chromosomes in the GnomAD database, including 127,974 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 0.49 ( 20928 hom., cov: 32)

Exomes 𝑓: 0.37 ( 107046 hom. )

Consequence

OSBPL10
NM_017784.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -6.33

Publications

17 publications found

Variant links:

Genes affected

OSBPL10 (HGNC:16395): (oxysterol binding protein like 10) This gene encodes a member of the oxysterol-binding protein (OSBP) family, a group of intracellular lipid receptors. Like most members, the encoded protein contains an N-terminal pleckstrin homology domain and a highly conserved C-terminal OSBP-like sterol-binding domain. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]

OSBPL10 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (REVEL=0.049).

BP7

Synonymous conserved (PhyloP=-6.33 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL10	NM_017784.5 link	c.1809G>A	p.Pro603Pro	synonymous_variant	Exon 9 of 12	ENST00000396556.7	NP_060254.2	Q9BXB5-1Q9NX98

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
OSBPL10	ENST00000396556.7 link	c.1809G>A	p.Pro603Pro	synonymous_variant	Exon 9 of 12	1	NM_017784.5	ENSP00000379804.2	Q9BXB5-1
OSBPL10	ENST00000438237.6 link	c.1617G>A	p.Pro539Pro	synonymous_variant	Exon 8 of 11	2		ENSP00000406124.2	Q9BXB5-2
OSBPL10	ENST00000429492.6 link	c.1113G>A	p.Pro371Pro	synonymous_variant	Exon 6 of 8	2		ENSP00000416078.2	H7C487

Frequencies

GnomAD3 genomes

AF:

0.490

AC:

74371

AN:

151886

Hom.:

20878

Cov.:

show subpopulations

Gnomad AFR

AF:

0.770

Gnomad AMI

AF:

0.285

Gnomad AMR

AF:

0.407

Gnomad ASJ

AF:

0.477

Gnomad EAS

AF:

0.677

Gnomad SAS

AF:

0.398

Gnomad FIN

AF:

0.380

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.350

Gnomad OTH

AF:

0.493

GnomAD2 exomes

AF:

0.421

AC:

105656

AN:

251254

AF XY:

0.414

show subpopulations

Gnomad AFR exome

AF:

0.776

Gnomad AMR exome

AF:

0.361

Gnomad ASJ exome

AF:

0.483

Gnomad EAS exome

AF:

0.678

Gnomad FIN exome

AF:

0.366

Gnomad NFE exome

AF:

0.358

Gnomad OTH exome

AF:

0.414

GnomAD4 exome

AF:

0.372

AC:

544358

AN:

1461686

Hom.:

107046

Cov.:

AF XY:

0.373

AC XY:

270859

AN XY:

727120

show subpopulations

African (AFR)

AF:

0.784

AC:

26234

AN:

33474

American (AMR)

AF:

0.367

AC:

16410

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.482

AC:

12597

AN:

26134

East Asian (EAS)

AF:

0.667

AC:

26457

AN:

39688

South Asian (SAS)

AF:

0.400

AC:

34510

AN:

86220

European-Finnish (FIN)

AF:

0.372

AC:

19866

AN:

53412

Middle Eastern (MID)

AF:

0.462

AC:

2664

AN:

5768

European-Non Finnish (NFE)

AF:

0.343

AC:

380831

AN:

1111880

Other (OTH)

AF:

0.410

AC:

24789

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

18510

37020

55530

74040

92550

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12478

24956

37434

49912

62390

<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:

0.490

AC:

74476

AN:

152004

Hom.:

20928

Cov.:

AF XY:

0.490

AC XY:

36375

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.771

AC:

31946

AN:

41452

American (AMR)

AF:

0.407

AC:

6218

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.477

AC:

1654

AN:

3466

East Asian (EAS)

AF:

0.676

AC:

3480

AN:

5148

South Asian (SAS)

AF:

0.399

AC:

1923

AN:

4820

European-Finnish (FIN)

AF:

0.380

AC:

4013

AN:

10564

Middle Eastern (MID)

AF:

0.463

AC:

136

AN:

294

European-Non Finnish (NFE)

AF:

0.350

AC:

23806

AN:

67958

Other (OTH)

AF:

0.494

AC:

1041

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1714

3427

5141

6854

8568

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

632

1264

1896

2528

3160

<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:

0.400

Hom.:

49632

Bravo

AF:

0.506

Asia WGS

AF:

0.536

AC:

1865

AN:

3478

EpiCase

AF:

0.367

EpiControl

AF:

0.366

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.030

(source)

DANN

Benign

0.62

PhyloP100

-6.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=97/3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over