dbSNP rs17178177: OSBPL5:c.*564G>C (chr11-3087641-C-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_020896.4(OSBPL5):c.*564G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,930 control chromosomes in the GnomAD database, including 875 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 0.10 ( 870 hom., cov: 33)

Exomes 𝑓: 0.11 ( 5 hom. )

Consequence

OSBPL5
NM_020896.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.440

Publications

4 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=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.118 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	UniProt
OSBPL5	NM_020896.4	MANE Select	c.*564G>C	3_prime_UTR	Exon 22 of 22	NP_065947.1	Q9H0X9-1
OSBPL5	NM_001144063.2		c.*564G>C	3_prime_UTR	Exon 21 of 21	NP_001137535.1	Q9H0X9-2
OSBPL5	NM_145638.3		c.*564G>C	3_prime_UTR	Exon 21 of 21	NP_663613.1	Q9H0X9-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
OSBPL5	ENST00000263650.12	TSL:1 MANE Select	c.*564G>C	3_prime_UTR	Exon 22 of 22	ENSP00000263650.7	Q9H0X9-1
OSBPL5	ENST00000389989.7	TSL:1	c.*564G>C	3_prime_UTR	Exon 21 of 21	ENSP00000374639.3	Q9H0X9-2
OSBPL5	ENST00000866647.1		c.*564G>C	3_prime_UTR	Exon 22 of 22	ENSP00000536706.1

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

15371

AN:

152042

Hom.:

871

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0990

Gnomad AMI

AF:

0.202

Gnomad AMR

AF:

0.0686

Gnomad ASJ

AF:

0.0593

Gnomad EAS

AF:

0.00289

Gnomad SAS

AF:

0.0892

Gnomad FIN

AF:

0.0961

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.120

Gnomad OTH

AF:

0.0932

GnomAD4 exome

AF:

0.106

AC:

AN:

774

Hom.:

Cov.:

AF XY:

0.116

AC XY:

AN XY:

464

show subpopulations

African (AFR)

AF:

0.0625

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:

0.135

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.109

AC:

AN:

604

Other (OTH)

AF:

0.148

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.101

AC:

15373

AN:

152156

Hom.:

870

Cov.:

AF XY:

0.0983

AC XY:

7316

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.0990

AC:

4103

AN:

41464

American (AMR)

AF:

0.0686

AC:

1049

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0593

AC:

206

AN:

3472

East Asian (EAS)

AF:

0.00290

AC:

AN:

5170

South Asian (SAS)

AF:

0.0892

AC:

431

AN:

4830

European-Finnish (FIN)

AF:

0.0961

AC:

1019

AN:

10608

Middle Eastern (MID)

AF:

0.0918

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.120

AC:

8148

AN:

68010

Other (OTH)

AF:

0.0908

AC:

192

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

739

1477

2216

2954

3693

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

178

356

534

712

890

<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:

0.109

Hom.:

116

Bravo

AF:

0.0986

Asia WGS

AF:

0.0420

AC:

148

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

5.5

(source)

DANN

Benign

0.49

PhyloP100

0.44

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