Variant 3-31748090-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017784.5(OSBPL10):c.760A>G(p.Asn254Asp) variant causes a missense change. The variant allele was found at a frequency of 0.453 in 1,612,980 control chromosomes in the GnomAD database, including 174,263 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.37 ( 13219 hom., cov: 32)

Exomes 𝑓: 0.46 ( 161044 hom. )

Consequence

OSBPL10
NM_017784.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.94

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=5.621795E-6).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL10	NM_017784.5 linkuse as main transcript	c.760A>G	p.Asn254Asp	missense_variant	5/12	ENST00000396556.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL10	ENST00000396556.7 linkuse as main transcript	c.760A>G	p.Asn254Asp	missense_variant	5/12	1	NM_017784.5	P2	Q9BXB5-1

Frequencies

GnomAD3 genomes

AF:

0.375

AC:

57006

AN:

151932

Hom.:

13220

Cov.:

show subpopulations

Gnomad AFR

AF:

0.107

Gnomad AMI

AF:

0.467

Gnomad AMR

AF:

0.531

Gnomad ASJ

AF:

0.403

Gnomad EAS

AF:

0.756

Gnomad SAS

AF:

0.511

Gnomad FIN

AF:

0.470

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.448

Gnomad OTH

AF:

0.378

GnomAD3 exomes

AF:

0.481

AC:

120098

AN:

249498

Hom.:

31579

AF XY:

0.479

AC XY:

64575

AN XY:

134808

show subpopulations

Gnomad AFR exome

AF:

0.102

Gnomad AMR exome

AF:

0.665

Gnomad ASJ exome

AF:

0.398

Gnomad EAS exome

AF:

0.755

Gnomad SAS exome

AF:

0.492

Gnomad FIN exome

AF:

0.475

Gnomad NFE exome

AF:

0.444

Gnomad OTH exome

AF:

0.437

GnomAD4 exome

AF:

0.461

AC:

672890

AN:

1460930

Hom.:

161044

Cov.:

AF XY:

0.461

AC XY:

335224

AN XY:

726690

show subpopulations

Gnomad4 AFR exome

AF:

0.0902

Gnomad4 AMR exome

AF:

0.647

Gnomad4 ASJ exome

AF:

0.398

Gnomad4 EAS exome

AF:

0.767

Gnomad4 SAS exome

AF:

0.496

Gnomad4 FIN exome

AF:

0.480

Gnomad4 NFE exome

AF:

0.453

Gnomad4 OTH exome

AF:

0.437

GnomAD4 genome

AF:

0.375

AC:

56998

AN:

152050

Hom.:

13219

Cov.:

AF XY:

0.382

AC XY:

28349

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.107

Gnomad4 AMR

AF:

0.531

Gnomad4 ASJ

AF:

0.403

Gnomad4 EAS

AF:

0.756

Gnomad4 SAS

AF:

0.509

Gnomad4 FIN

AF:

0.470

Gnomad4 NFE

AF:

0.448

Gnomad4 OTH

AF:

0.376

Alfa

AF:

0.434

Hom.:

37187

Bravo

AF:

0.368

TwinsUK

AF:

0.463

AC:

1716

ALSPAC

AF:

0.469

AC:

1808

ESP6500AA

AF:

0.116

AC:

511

ESP6500EA

AF:

0.439

AC:

3774

ExAC

AF:

0.466

AC:

56584

Asia WGS

AF:

0.535

AC:

1861

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.70

BayesDel_noAF

Benign

-0.63

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.019

T;.;T

Eigen

Benign

-0.13

Eigen_PC

Benign

0.012

FATHMM_MKL

Uncertain

0.90

LIST_S2

Benign

0.50

T;T;T

MetaRNN

Benign

0.0000056

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.86

L;.;.

MutationTaster

Benign

0.44

P;P

PrimateAI

Uncertain

0.53

PROVEAN

Benign

-1.4

N;N;N

REVEL

Benign

0.094

Sift

Benign

0.64

T;T;T

Sift4G

Benign

0.41

T;T;T

Polyphen

0.011

B;.;.

Vest4

0.061

MPC

0.45

ClinPred

0.035

GERP RS

4.5

Varity_R

0.13

gMVP

0.42

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