dbSNP rs935431: OSBPL5:c.*138C>T (chr11-3088067-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020896.4(OSBPL5):c.*138C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 804,802 control chromosomes in the GnomAD database, including 5,417 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 0.096 ( 808 hom., cov: 34)

Exomes 𝑓: 0.11 ( 4609 hom. )

Consequence

OSBPL5
NM_020896.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.967

Publications

5 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL5	NM_020896.4 link	c.*138C>T		3_prime_UTR_variant	Exon 22 of 22	ENST00000263650.12	NP_065947.1	Q9H0X9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSBPL5	ENST00000263650.12 link	c.*138C>T		3_prime_UTR_variant	Exon 22 of 22	1	NM_020896.4	ENSP00000263650.7		Q9H0X9-1

Frequencies

GnomAD3 genomes

AF:

0.0960

AC:

14598

AN:

152108

Hom.:

809

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0573

Gnomad AMI

AF:

0.0724

Gnomad AMR

AF:

0.165

Gnomad ASJ

AF:

0.135

Gnomad EAS

AF:

0.0141

Gnomad SAS

AF:

0.0458

Gnomad FIN

AF:

0.0633

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.116

Gnomad OTH

AF:

0.130

GnomAD4 exome

AF:

0.110

AC:

71576

AN:

652576

Hom.:

4609

Cov.:

AF XY:

0.108

AC XY:

35220

AN XY:

326490

show subpopulations

African (AFR)

AF:

0.0602

AC:

876

AN:

14546

American (AMR)

AF:

0.159

AC:

1920

AN:

12064

Ashkenazi Jewish (ASJ)

AF:

0.139

AC:

1910

AN:

13712

East Asian (EAS)

AF:

0.00505

AC:

135

AN:

26714

South Asian (SAS)

AF:

0.0510

AC:

1826

AN:

35818

European-Finnish (FIN)

AF:

0.0664

AC:

1868

AN:

28132

Middle Eastern (MID)

AF:

0.141

AC:

318

AN:

2260

European-Non Finnish (NFE)

AF:

0.121

AC:

59193

AN:

487802

Other (OTH)

AF:

0.112

AC:

3530

AN:

31528

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

3110

6219

9329

12438

15548

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1716

3432

5148

6864

8580

<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:

0.0959

AC:

14594

AN:

152226

Hom.:

808

Cov.:

AF XY:

0.0917

AC XY:

6822

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.0571

AC:

2373

AN:

41548

American (AMR)

AF:

0.165

AC:

2518

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.135

AC:

468

AN:

3470

East Asian (EAS)

AF:

0.0139

AC:

AN:

5170

South Asian (SAS)

AF:

0.0460

AC:

222

AN:

4824

European-Finnish (FIN)

AF:

0.0633

AC:

671

AN:

10596

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.116

AC:

7899

AN:

68004

Other (OTH)

AF:

0.128

AC:

270

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

692

1385

2077

2770

3462

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

162

324

486

648

810

<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:

0.0453

Hom.:

Bravo

AF:

0.104

Asia WGS

AF:

0.0320

AC:

113

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.048

(source)

DANN

Benign

0.75

PhyloP100

-0.97

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over