Genetic Variant OSBPL10:c.729+32290A>G (chr3-31797750-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_017784.5(OSBPL10):c.729+32290A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 454,144 control chromosomes in the GnomAD database, including 133,239 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 0.78 ( 46549 hom., cov: 32)

Exomes 𝑓: 0.76 ( 86690 hom. )

Consequence

OSBPL10
NM_017784.5 intron

Scores

Splicing: ADA: 0.00005103

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.712

Publications

11 publications found

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 was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL10	NM_017784.5 link	c.729+32290A>G		intron_variant	Intron 4 of 11	ENST00000396556.7	NP_060254.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSBPL10	ENST00000396556.7 link	c.729+32290A>G		intron_variant	Intron 4 of 11	1	NM_017784.5	ENSP00000379804.2

Frequencies

GnomAD3 genomes

AF:

0.780

AC:

118594

AN:

152022

Hom.:

46498

Cov.:

show subpopulations

Gnomad AFR

AF:

0.863

Gnomad AMI

AF:

0.681

Gnomad AMR

AF:

0.765

Gnomad ASJ

AF:

0.761

Gnomad EAS

AF:

0.806

Gnomad SAS

AF:

0.774

Gnomad FIN

AF:

0.761

Gnomad MID

AF:

0.750

Gnomad NFE

AF:

0.738

Gnomad OTH

AF:

0.757

GnomAD2 exomes

AF:

0.764

AC:

104141

AN:

136272

AF XY:

0.765

show subpopulations

Gnomad AFR exome

AF:

0.865

Gnomad AMR exome

AF:

0.754

Gnomad ASJ exome

AF:

0.767

Gnomad EAS exome

AF:

0.830

Gnomad FIN exome

AF:

0.754

Gnomad NFE exome

AF:

0.741

Gnomad OTH exome

AF:

0.737

GnomAD4 exome

AF:

0.756

AC:

228462

AN:

302004

Hom.:

86690

Cov.:

AF XY:

0.759

AC XY:

130441

AN XY:

171928

show subpopulations

African (AFR)

AF:

0.868

AC:

7406

AN:

8532

American (AMR)

AF:

0.755

AC:

20458

AN:

27108

Ashkenazi Jewish (ASJ)

AF:

0.765

AC:

8210

AN:

10738

East Asian (EAS)

AF:

0.822

AC:

7496

AN:

9124

South Asian (SAS)

AF:

0.777

AC:

46143

AN:

59378

European-Finnish (FIN)

AF:

0.745

AC:

9508

AN:

12762

Middle Eastern (MID)

AF:

0.756

AC:

2098

AN:

2776

European-Non Finnish (NFE)

AF:

0.740

AC:

116511

AN:

157452

Other (OTH)

AF:

0.752

AC:

10632

AN:

14134

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

2563

5125

7688

10250

12813

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

618

1236

1854

2472

3090

<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:

0.780

AC:

118701

AN:

152140

Hom.:

46549

Cov.:

AF XY:

0.782

AC XY:

58106

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.863

AC:

35827

AN:

41526

American (AMR)

AF:

0.765

AC:

11696

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.761

AC:

2642

AN:

3472

East Asian (EAS)

AF:

0.806

AC:

4157

AN:

5160

South Asian (SAS)

AF:

0.773

AC:

3716

AN:

4806

European-Finnish (FIN)

AF:

0.761

AC:

8042

AN:

10572

Middle Eastern (MID)

AF:

0.755

AC:

222

AN:

294

European-Non Finnish (NFE)

AF:

0.738

AC:

50177

AN:

67992

Other (OTH)

AF:

0.757

AC:

1601

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1321

2643

3964

5286

6607

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

864

1728

2592

3456

4320

<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:

0.754

Hom.:

139790

Bravo

AF:

0.784

Asia WGS

AF:

0.799

AC:

2781

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

(source)

DANN

Benign

0.59

PhyloP100

-0.71

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000051

dbscSNV1_RF

Benign

0.0

SpliceAI score (max)

0.83

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.83

Position offset: 5

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

Computational scores

Splicing

Publications

Other links and lift over