Variant chr11-3090636-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_020896.4(OSBPL5):c.2320G>A(p.Ala774Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 1,612,596 control chromosomes in the GnomAD database, including 34,431 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict 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 0.19 ( 3158 hom., cov: 34)

Exomes 𝑓: 0.20 ( 31273 hom. )

Consequence

OSBPL5
NM_020896.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.05

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0033494234).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL5	NM_020896.4 linkuse as main transcript	c.2320G>A	p.Ala774Thr	missense_variant	20/22	ENST00000263650.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL5	ENST00000263650.12 linkuse as main transcript	c.2320G>A	p.Ala774Thr	missense_variant	20/22	1	NM_020896.4	P1	Q9H0X9-1

Frequencies

GnomAD3 genomes

AF:

0.192

AC:

29252

AN:

152152

Hom.:

3157

Cov.:

show subpopulations

Gnomad AFR

AF:

0.160

Gnomad AMI

AF:

0.226

Gnomad AMR

AF:

0.140

Gnomad ASJ

AF:

0.194

Gnomad EAS

AF:

0.0343

Gnomad SAS

AF:

0.267

Gnomad FIN

AF:

0.372

Gnomad MID

AF:

0.204

Gnomad NFE

AF:

0.203

Gnomad OTH

AF:

0.161

GnomAD3 exomes

AF:

0.194

AC:

48302

AN:

248928

Hom.:

5575

AF XY:

0.203

AC XY:

27374

AN XY:

135180

show subpopulations

Gnomad AFR exome

AF:

0.157

Gnomad AMR exome

AF:

0.0902

Gnomad ASJ exome

AF:

0.180

Gnomad EAS exome

AF:

0.0279

Gnomad SAS exome

AF:

0.283

Gnomad FIN exome

AF:

0.358

Gnomad NFE exome

AF:

0.204

Gnomad OTH exome

AF:

0.195

GnomAD4 exome

AF:

0.200

AC:

291829

AN:

1460324

Hom.:

31273

Cov.:

AF XY:

0.203

AC XY:

147227

AN XY:

726460

show subpopulations

Gnomad4 AFR exome

AF:

0.157

Gnomad4 AMR exome

AF:

0.0951

Gnomad4 ASJ exome

AF:

0.183

Gnomad4 EAS exome

AF:

0.0611

Gnomad4 SAS exome

AF:

0.278

Gnomad4 FIN exome

AF:

0.358

Gnomad4 NFE exome

AF:

0.198

Gnomad4 OTH exome

AF:

0.189

GnomAD4 genome

AF:

0.192

AC:

29267

AN:

152272

Hom.:

3158

Cov.:

AF XY:

0.199

AC XY:

14817

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.160

Gnomad4 AMR

AF:

0.140

Gnomad4 ASJ

AF:

0.194

Gnomad4 EAS

AF:

0.0344

Gnomad4 SAS

AF:

0.267

Gnomad4 FIN

AF:

0.372

Gnomad4 NFE

AF:

0.203

Gnomad4 OTH

AF:

0.163

Alfa

AF:

0.195

Hom.:

1394

Bravo

AF:

0.166

TwinsUK

AF:

0.199

AC:

739

ALSPAC

AF:

0.196

AC:

756

ESP6500AA

AF:

0.155

AC:

683

ESP6500EA

AF:

0.194

AC:

1668

ExAC

AF:

0.198

AC:

23970

Asia WGS

AF:

0.159

AC:

550

AN:

3478

EpiCase

AF:

0.195

EpiControl

AF:

0.198

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.075

BayesDel_addAF

Benign

-0.75

BayesDel_noAF

Benign

-0.71

CADD

Benign

DANN

Benign

0.70

DEOGEN2

Benign

0.0033

.;T;.;T;.;.

Eigen

Benign

-0.70

Eigen_PC

Benign

-0.55

FATHMM_MKL

Benign

0.30

LIST_S2

Benign

0.54

T;T;.;T;T;T

MetaRNN

Benign

0.0033

T;T;T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.90

.;N;.;.;.;.

MutationTaster

Benign

1.0

P;P;P;P;P;P

PrimateAI

Uncertain

0.55

PROVEAN

Benign

-0.080

N;N;N;N;N;N

REVEL

Benign

0.066

Sift

Benign

0.59

T;T;T;T;T;T

Sift4G

Benign

1.0

T;T;T;T;T;T

Polyphen

0.0

.;B;.;.;.;.

Vest4

0.026

MPC

0.14

ClinPred

0.0098

GERP RS

2.7

Varity_R

0.055

gMVP

0.19

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