22-30888236-T-C

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7

The NM_030758.4(OSBP2):c.1314T>C(p.Thr438Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,609,720 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000013 ( 1 hom. )

Consequence

OSBP2
NM_030758.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.633

Publications

0 publications found

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:

LOC107985544 (HGNC:):

LOC107985544 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -5 ACMG points.

BP4

Computational evidence support a benign effect (REVEL=0.024).

BP6

Variant 22-30888236-T-C is Benign according to our data. Variant chr22-30888236-T-C is described in CliVar as Likely_benign. Clinvar id is 2653061.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-30888236-T-C is described in CliVar as Likely_benign. Clinvar id is 2653061.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-30888236-T-C is described in CliVar as Likely_benign. Clinvar id is 2653061.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-30888236-T-C is described in CliVar as Likely_benign. Clinvar id is 2653061.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-30888236-T-C is described in CliVar as Likely_benign. Clinvar id is 2653061.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-30888236-T-C is described in CliVar as Likely_benign. Clinvar id is 2653061.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-30888236-T-C is described in CliVar as Likely_benign. Clinvar id is 2653061.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-30888236-T-C is described in CliVar as Likely_benign. Clinvar id is 2653061.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-30888236-T-C is described in CliVar as Likely_benign. Clinvar id is 2653061.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-30888236-T-C is described in CliVar as Likely_benign. Clinvar id is 2653061.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-30888236-T-C is described in CliVar as Likely_benign. Clinvar id is 2653061.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-30888236-T-C is described in CliVar as Likely_benign. Clinvar id is 2653061.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-30888236-T-C is described in CliVar as Likely_benign. Clinvar id is 2653061.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-30888236-T-C is described in CliVar as Likely_benign. Clinvar id is 2653061.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-30888236-T-C is described in CliVar as Likely_benign. Clinvar id is 2653061.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-30888236-T-C is described in CliVar as Likely_benign. Clinvar id is 2653061.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-30888236-T-C is described in CliVar as Likely_benign. Clinvar id is 2653061.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-30888236-T-C is described in CliVar as Likely_benign. Clinvar id is 2653061.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-30888236-T-C is described in CliVar as Likely_benign. Clinvar id is 2653061.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-30888236-T-C is described in CliVar as Likely_benign. Clinvar id is 2653061.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-30888236-T-C is described in CliVar as Likely_benign. Clinvar id is 2653061.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-30888236-T-C is described in CliVar as Likely_benign. Clinvar id is 2653061.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.633 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBP2	NM_030758.4 link	c.1314T>C	p.Thr438Thr	synonymous_variant	Exon 5 of 14	ENST00000332585.11	NP_110385.1	Q969R2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSBP2	ENST00000332585.11 link	c.1314T>C	p.Thr438Thr	synonymous_variant	Exon 5 of 14	1	NM_030758.4	ENSP00000332576.6		Q969R2-1

Frequencies

GnomAD3 genomes

AF:

0.0000132

AC:

AN:

152072

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000415

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000241

AC:

AN:

249426

AF XY:

0.0000369

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000130

AC:

AN:

1457530

Hom.:

Cov.:

AF XY:

0.0000207

AC XY:

AN XY:

725538

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33374

American (AMR)

AF:

0.00

AC:

AN:

44696

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26114

East Asian (EAS)

AF:

0.00

AC:

AN:

39676

South Asian (SAS)

AF:

0.000209

AC:

AN:

86152

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53370

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5758

European-Non Finnish (NFE)

AF:

9.02e-7

AC:

AN:

1108146

Other (OTH)

AF:

0.00

AC:

AN:

60244

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.449

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.0000131

AC:

AN:

152190

Hom.:

Cov.:

AF XY:

0.0000134

AC XY:

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41518

American (AMR)

AF:

0.00

AC:

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5176

South Asian (SAS)

AF:

0.000415

AC:

AN:

4814

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10598

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

68008

Other (OTH)

AF:

0.00

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jul 01, 2022

CeGaT Center for Human Genetics Tuebingen

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

OSBP2: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

9.0

(source)

DANN

Benign

0.71

PhyloP100

0.63

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over