Variant chr22-30870559-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_030758.4(OSBP2):c.984T>C(p.Ala328Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.631 in 1,613,652 control chromosomes in the GnomAD database, including 323,438 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.66 ( 33615 hom., cov: 32)

Exomes 𝑓: 0.63 ( 289823 hom. )

Consequence

OSBP2
NM_030758.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -4.61

Variant links:

Genes affected

OSBP2 (HGNC:8504): (oxysterol binding protein 2) The protein encoded by this gene contains a pleckstrin homology (PH) domain and an oxysterol-binding region. It binds oxysterols such as 7-ketocholesterol and may inhibit their cytotoxicity. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Sep 2013]

OSBP2 links:

OSBP2 (HGNC:):

OSBP2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 22-30870559-T-C is Benign according to our data. Variant chr22-30870559-T-C is described in ClinVar as [Benign]. Clinvar id is 1261963.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-4.61 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OSBP2	NM_030758.4 linkuse as main transcript	c.984T>C	p.Ala328Ala	synonymous_variant	3/14	ENST00000332585.11	NP_110385.1	Q969R2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OSBP2	ENST00000332585.11 linkuse as main transcript	c.984T>C	p.Ala328Ala	synonymous_variant	3/14	1	NM_030758.4	ENSP00000332576.6		Q969R2-1

Frequencies

GnomAD3 genomes

AF:

0.661

AC:

100464

AN:

151930

Hom.:

33562

Cov.:

show subpopulations

Gnomad AFR

AF:

0.710

Gnomad AMI

AF:

0.561

Gnomad AMR

AF:

0.642

Gnomad ASJ

AF:

0.617

Gnomad EAS

AF:

0.816

Gnomad SAS

AF:

0.647

Gnomad FIN

AF:

0.754

Gnomad MID

AF:

0.639

Gnomad NFE

AF:

0.615

Gnomad OTH

AF:

0.644

GnomAD3 exomes

AF:

0.657

AC:

163431

AN:

248920

Hom.:

54163

AF XY:

0.653

AC XY:

88187

AN XY:

135152

show subpopulations

Gnomad AFR exome

AF:

0.719

Gnomad AMR exome

AF:

0.635

Gnomad ASJ exome

AF:

0.602

Gnomad EAS exome

AF:

0.823

Gnomad SAS exome

AF:

0.639

Gnomad FIN exome

AF:

0.749

Gnomad NFE exome

AF:

0.621

Gnomad OTH exome

AF:

0.630

GnomAD4 exome

AF:

0.628

AC:

917358

AN:

1461604

Hom.:

289823

Cov.:

AF XY:

0.628

AC XY:

456745

AN XY:

727114

show subpopulations

Gnomad4 AFR exome

AF:

0.719

Gnomad4 AMR exome

AF:

0.638

Gnomad4 ASJ exome

AF:

0.595

Gnomad4 EAS exome

AF:

0.821

Gnomad4 SAS exome

AF:

0.642

Gnomad4 FIN exome

AF:

0.734

Gnomad4 NFE exome

AF:

0.612

Gnomad4 OTH exome

AF:

0.630

GnomAD4 genome

AF:

0.661

AC:

100576

AN:

152048

Hom.:

33615

Cov.:

AF XY:

0.666

AC XY:

49483

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.711

Gnomad4 AMR

AF:

0.642

Gnomad4 ASJ

AF:

0.617

Gnomad4 EAS

AF:

0.816

Gnomad4 SAS

AF:

0.647

Gnomad4 FIN

AF:

0.754

Gnomad4 NFE

AF:

0.615

Gnomad4 OTH

AF:

0.647

Alfa

AF:

0.626

Hom.:

31439

Bravo

AF:

0.658

Asia WGS

AF:

0.755

AC:

2624

AN:

3478

EpiCase

AF:

0.618

EpiControl

AF:

0.624

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 07, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.082

DANN

Benign

0.59

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over