dbSNP rs8813: OSBPL5:c.*929C>T (chr11-3087276-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.*929C>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 0.165 in 153,308 control chromosomes in the GnomAD database, including 2,658 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 0.17 ( 2640 hom., cov: 34)

Exomes 𝑓: 0.18 ( 18 hom. )

Consequence

OSBPL5
NM_020896.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.46

Publications

13 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:

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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=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL5	NM_020896.4 link	c.*929C>T		3_prime_UTR_variant	Exon 22 of 22	ENST00000263650.12	NP_065947.1	Q9H0X9-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
OSBPL5	ENST00000263650.12 link	c.*929C>T	3_prime_UTR_variant	Exon 22 of 22	1	NM_020896.4	ENSP00000263650.7	Q9H0X9-1
OSBPL5	ENST00000389989.7 link	c.*929C>T	3_prime_UTR_variant	Exon 21 of 21	1		ENSP00000374639.3	Q9H0X9-2
OSBPL5	ENST00000478260.5 link	c.*929C>T	3_prime_UTR_variant	Exon 8 of 8	2		ENSP00000437141.1	E9PNH0
OSBPL5	ENST00000534454.5 link	c.*535C>T	downstream_gene_variant		5		ENSP00000431412.1	H0YCD7

Frequencies

GnomAD3 genomes

AF:

0.165

AC:

25127

AN:

152100

Hom.:

2639

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0565

Gnomad AMI

AF:

0.365

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.185

Gnomad EAS

AF:

0.00462

Gnomad SAS

AF:

0.130

Gnomad FIN

AF:

0.243

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.238

Gnomad OTH

AF:

0.153

GnomAD4 exome

AF:

0.183

AC:

199

AN:

1090

Hom.:

Cov.:

AF XY:

0.186

AC XY:

110

AN XY:

590

show subpopulations

African (AFR)

AF:

0.0357

AC:

AN:

American (AMR)

AF:

0.125

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.158

AC:

AN:

European-Finnish (FIN)

AF:

0.228

AC:

AN:

268

Middle Eastern (MID)

AF:

0.178

AC:

AN:

422

European-Non Finnish (NFE)

AF:

0.181

AC:

AN:

254

Other (OTH)

AF:

0.132

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.165

AC:

25126

AN:

152218

Hom.:

2640

Cov.:

AF XY:

0.163

AC XY:

12147

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.0564

AC:

2344

AN:

41552

American (AMR)

AF:

0.133

AC:

2033

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.185

AC:

641

AN:

3470

East Asian (EAS)

AF:

0.00463

AC:

AN:

5180

South Asian (SAS)

AF:

0.131

AC:

632

AN:

4826

European-Finnish (FIN)

AF:

0.243

AC:

2577

AN:

10590

Middle Eastern (MID)

AF:

0.180

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.238

AC:

16172

AN:

67990

Other (OTH)

AF:

0.151

AC:

318

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1040

2080

3120

4160

5200

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

266

532

798

1064

1330

<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:

0.213

Hom.:

3283

Bravo

AF:

0.151

Asia WGS

AF:

0.0630

AC:

221

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

(source)

DANN

Benign

0.87

PhyloP100

1.5

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over