Genetic Variant OSBPL10:c.729+32397T>C (chr3-31797643-A-G) – 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+32397T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 344,112 control chromosomes in the GnomAD database, including 72,039 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 0.58 ( 27621 hom., cov: 32)

Exomes 𝑓: 0.68 ( 44418 hom. )

Consequence

OSBPL10
NM_017784.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.311

Publications

4 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=-0.65).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017784.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL10	NM_017784.5	MANE Select	c.729+32397T>C		intron	N/A	NP_060254.2
	OSBPL10	NM_001174060.2		c.538-49523T>C		intron	N/A	NP_001167531.1	Q9BXB5-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
OSBPL10	ENST00000396556.7	TSL:1 MANE Select	c.729+32397T>C	intron	N/A	ENSP00000379804.2	Q9BXB5-1
OSBPL10	ENST00000959571.1		c.624+112T>C	intron	N/A	ENSP00000629630.1
OSBPL10	ENST00000911816.1		c.729+32397T>C	intron	N/A	ENSP00000581875.1

Frequencies

GnomAD3 genomes

AF:

0.583

AC:

88602

AN:

152006

Hom.:

27610

Cov.:

show subpopulations

Gnomad AFR

AF:

0.339

Gnomad AMI

AF:

0.555

Gnomad AMR

AF:

0.672

Gnomad ASJ

AF:

0.687

Gnomad EAS

AF:

0.787

Gnomad SAS

AF:

0.721

Gnomad FIN

AF:

0.678

Gnomad MID

AF:

0.604

Gnomad NFE

AF:

0.665

Gnomad OTH

AF:

0.600

GnomAD4 exome

AF:

0.676

AC:

129769

AN:

191988

Hom.:

44418

AF XY:

0.683

AC XY:

72844

AN XY:

106668

show subpopulations

African (AFR)

AF:

0.350

AC:

1687

AN:

4820

American (AMR)

AF:

0.697

AC:

9939

AN:

14252

Ashkenazi Jewish (ASJ)

AF:

0.697

AC:

3767

AN:

5408

East Asian (EAS)

AF:

0.809

AC:

5225

AN:

6458

South Asian (SAS)

AF:

0.714

AC:

29594

AN:

41432

European-Finnish (FIN)

AF:

0.660

AC:

6001

AN:

9088

Middle Eastern (MID)

AF:

0.668

AC:

954

AN:

1428

European-Non Finnish (NFE)

AF:

0.666

AC:

66711

AN:

100182

Other (OTH)

AF:

0.660

AC:

5891

AN:

8920

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

1871

3743

5614

7486

9357

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

414

828

1242

1656

2070

<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:

0.583

AC:

88625

AN:

152124

Hom.:

27621

Cov.:

AF XY:

0.589

AC XY:

43815

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.339

AC:

14064

AN:

41500

American (AMR)

AF:

0.673

AC:

10286

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.687

AC:

2380

AN:

3464

East Asian (EAS)

AF:

0.786

AC:

4063

AN:

5166

South Asian (SAS)

AF:

0.720

AC:

3476

AN:

4826

European-Finnish (FIN)

AF:

0.678

AC:

7185

AN:

10592

Middle Eastern (MID)

AF:

0.622

AC:

183

AN:

294

European-Non Finnish (NFE)

AF:

0.665

AC:

45217

AN:

67974

Other (OTH)

AF:

0.601

AC:

1266

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1749

3497

5246

6994

8743

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

746

1492

2238

2984

3730

<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:

0.641

Hom.:

126355

Bravo

AF:

0.571

Asia WGS

AF:

0.714

AC:

2481

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

(source)

DANN

Benign

0.91

PhyloP100

0.31

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over