dbSNP rs1053746: OSBPL5:c.*750C>T (chr11-3087455-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.*750C>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 0.0415 in 154,368 control chromosomes in the GnomAD database, including 167 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 0.042 ( 165 hom., cov: 33)

Exomes 𝑓: 0.029 ( 2 hom. )

Consequence

OSBPL5
NM_020896.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.544

Publications

3 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=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0674 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020896.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
OSBPL5	NM_020896.4	MANE Select	c.*750C>T	3_prime_UTR	Exon 22 of 22	NP_065947.1
OSBPL5	NM_001144063.2		c.*750C>T	3_prime_UTR	Exon 21 of 21	NP_001137535.1
OSBPL5	NM_145638.3		c.*750C>T	3_prime_UTR	Exon 21 of 21	NP_663613.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
OSBPL5	ENST00000263650.12	TSL:1 MANE Select	c.*750C>T	3_prime_UTR	Exon 22 of 22	ENSP00000263650.7
OSBPL5	ENST00000389989.7	TSL:1	c.*750C>T	3_prime_UTR	Exon 21 of 21	ENSP00000374639.3
OSBPL5	ENST00000534454.5	TSL:5	c.*356C>T	3_prime_UTR	Exon 12 of 12	ENSP00000431412.1

Frequencies

GnomAD3 genomes

AF:

0.0416

AC:

6329

AN:

152076

Hom.:

165

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0696

Gnomad AMI

AF:

0.147

Gnomad AMR

AF:

0.0180

Gnomad ASJ

AF:

0.0531

Gnomad EAS

AF:

0.00290

Gnomad SAS

AF:

0.0705

Gnomad FIN

AF:

0.0382

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0299

Gnomad OTH

AF:

0.0288

GnomAD4 exome

AF:

0.0290

AC:

AN:

2174

Hom.:

Cov.:

AF XY:

0.0335

AC XY:

AN XY:

1104

show subpopulations

African (AFR)

AF:

0.0286

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.0938

AC:

AN:

European-Finnish (FIN)

AF:

0.0556

AC:

AN:

Middle Eastern (MID)

AF:

0.0236

AC:

AN:

1484

European-Non Finnish (NFE)

AF:

0.0120

AC:

AN:

250

Other (OTH)

AF:

0.0536

AC:

AN:

168

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.522

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:

0.0417

AC:

6342

AN:

152194

Hom.:

165

Cov.:

AF XY:

0.0418

AC XY:

3111

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.0695

AC:

2887

AN:

41516

American (AMR)

AF:

0.0179

AC:

274

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0531

AC:

184

AN:

3468

East Asian (EAS)

AF:

0.00291

AC:

AN:

5162

South Asian (SAS)

AF:

0.0706

AC:

341

AN:

4830

European-Finnish (FIN)

AF:

0.0382

AC:

405

AN:

10606

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0299

AC:

2032

AN:

68010

Other (OTH)

AF:

0.0318

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

308

616

923

1231

1539

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

216

288

360

<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:

0.0326

Hom.:

249

Bravo

AF:

0.0396

Asia WGS

AF:

0.0420

AC:

147

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.037

(source)

DANN

Benign

0.78

PhyloP100

-0.54

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