Genetic Variant OSBPL10:p.Pro603Pro (chr3-31670901-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

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

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 made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

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

GnomAD3 exomes

AF:

0.421

AC:

105656

AN:

251254

Hom.:

24403

AF XY:

0.414

AC XY:

56197

AN XY:

135798

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 SAS exome

AF:

0.397

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

Gnomad4 AFR exome

AF:

0.784

Gnomad4 AMR exome

AF:

0.367

Gnomad4 ASJ exome

AF:

0.482

Gnomad4 EAS exome

AF:

0.667

Gnomad4 SAS exome

AF:

0.400

Gnomad4 FIN exome

AF:

0.372

Gnomad4 NFE exome

AF:

0.343

Gnomad4 OTH exome

AF:

0.410

GnomAD4 genome

AF:

0.490

AC:

74476

AN:

152004

Hom.:

20928

Cov.:

AF XY:

0.490

AC XY:

36375

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.771

Gnomad4 AMR

AF:

0.407

Gnomad4 ASJ

AF:

0.477

Gnomad4 EAS

AF:

0.676

Gnomad4 SAS

AF:

0.399

Gnomad4 FIN

AF:

0.380

Gnomad4 NFE

AF:

0.350

Gnomad4 OTH

AF:

0.494

Alfa

AF:

0.378

Hom.:

20693

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

DANN

Benign

0.62

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

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