Genetic Variant OSBPL6:p.Ser290Ser (chr2-178339070-G-A) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_032523.4(OSBPL6):c.870G>A(p.Ser290Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.917 in 1,610,878 control chromosomes in the GnomAD database, including 677,525 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 0.91 ( 63527 hom., cov: 32)

Exomes 𝑓: 0.92 ( 613998 hom. )

Consequence

OSBPL6
NM_032523.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.25

Publications

21 publications found

Variant links:

Genes affected

OSBPL6 (HGNC:16388): (oxysterol binding protein like 6) This gene encodes a member of the oxysterol-binding protein (OSBP) family, a group of intracellular lipid receptors. Most members contain an N-terminal pleckstrin homology domain and a highly conserved C-terminal OSBP-like sterol-binding domain. Transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

OSBPL6 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.32).

BP7

Synonymous conserved (PhyloP=1.25 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL6	NM_032523.4 link	c.870G>A	p.Ser290Ser	synonymous_variant	Exon 10 of 25	ENST00000190611.9	NP_115912.1	Q9BZF3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSBPL6	ENST00000190611.9 link	c.870G>A	p.Ser290Ser	synonymous_variant	Exon 10 of 25	1	NM_032523.4	ENSP00000190611.4		Q9BZF3-1

Frequencies

GnomAD3 genomes

AF:

0.913

AC:

138928

AN:

152166

Hom.:

63477

Cov.:

show subpopulations

Gnomad AFR

AF:

0.888

Gnomad AMI

AF:

0.934

Gnomad AMR

AF:

0.923

Gnomad ASJ

AF:

0.905

Gnomad EAS

AF:

0.969

Gnomad SAS

AF:

0.951

Gnomad FIN

AF:

0.948

Gnomad MID

AF:

0.885

Gnomad NFE

AF:

0.914

Gnomad OTH

AF:

0.900

GnomAD2 exomes

AF:

0.928

AC:

232437

AN:

250410

AF XY:

0.928

show subpopulations

Gnomad AFR exome

AF:

0.890

Gnomad AMR exome

AF:

0.944

Gnomad ASJ exome

AF:

0.907

Gnomad EAS exome

AF:

0.967

Gnomad FIN exome

AF:

0.946

Gnomad NFE exome

AF:

0.915

Gnomad OTH exome

AF:

0.922

GnomAD4 exome

AF:

0.917

AC:

1338071

AN:

1458592

Hom.:

613998

Cov.:

AF XY:

0.918

AC XY:

666454

AN XY:

725754

show subpopulations

African (AFR)

AF:

0.891

AC:

29731

AN:

33380

American (AMR)

AF:

0.941

AC:

41971

AN:

44606

Ashkenazi Jewish (ASJ)

AF:

0.907

AC:

23690

AN:

26112

East Asian (EAS)

AF:

0.973

AC:

38552

AN:

39618

South Asian (SAS)

AF:

0.952

AC:

81964

AN:

86090

European-Finnish (FIN)

AF:

0.943

AC:

50316

AN:

53330

Middle Eastern (MID)

AF:

0.898

AC:

5157

AN:

5742

European-Non Finnish (NFE)

AF:

0.912

AC:

1011622

AN:

1109430

Other (OTH)

AF:

0.913

AC:

55068

AN:

60284

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.452

Heterozygous variant carriers

5232

10464

15695

20927

26159

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

21438

42876

64314

85752

107190

<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:

0.913

AC:

139036

AN:

152286

Hom.:

63527

Cov.:

AF XY:

0.916

AC XY:

68169

AN XY:

74458

show subpopulations

African (AFR)

AF:

0.888

AC:

36894

AN:

41554

American (AMR)

AF:

0.923

AC:

14118

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.905

AC:

3139

AN:

3468

East Asian (EAS)

AF:

0.969

AC:

5025

AN:

5184

South Asian (SAS)

AF:

0.951

AC:

4591

AN:

4828

European-Finnish (FIN)

AF:

0.948

AC:

10060

AN:

10614

Middle Eastern (MID)

AF:

0.898

AC:

264

AN:

294

European-Non Finnish (NFE)

AF:

0.914

AC:

62192

AN:

68028

Other (OTH)

AF:

0.899

AC:

1901

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

633

1266

1899

2532

3165

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

910

1820

2730

3640

4550

<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:

0.913

Hom.:

138548

Bravo

AF:

0.910

Asia WGS

AF:

0.954

AC:

3318

AN:

3478

EpiCase

AF:

0.905

EpiControl

AF:

0.904

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.32

CADD

Benign

9.8

(source)

DANN

Benign

0.62

PhyloP100

1.2

Mutation Taster

=84/16

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over