rs9853939

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017784.5(OSBPL10):​c.281+32904T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,064 control chromosomes in the GnomAD database, including 26,925 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 0.57 ( 26925 hom., cov: 32)

Consequence

OSBPL10
NM_017784.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0390
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OSBPL10NM_017784.5 linkc.281+32904T>G intron_variant Intron 1 of 11 ENST00000396556.7 NP_060254.2 Q9BXB5-1Q9NX98

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OSBPL10ENST00000396556.7 linkc.281+32904T>G intron_variant Intron 1 of 11 1 NM_017784.5 ENSP00000379804.2 Q9BXB5-1

Frequencies

GnomAD3 genomes
AF:
0.568
AC:
86324
AN:
151946
Hom.:
26858
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.842
Gnomad AMI
AF:
0.395
Gnomad AMR
AF:
0.517
Gnomad ASJ
AF:
0.410
Gnomad EAS
AF:
0.527
Gnomad SAS
AF:
0.568
Gnomad FIN
AF:
0.482
Gnomad MID
AF:
0.525
Gnomad NFE
AF:
0.441
Gnomad OTH
AF:
0.545
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.569
AC:
86449
AN:
152064
Hom.:
26925
Cov.:
32
AF XY:
0.571
AC XY:
42465
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.843
Gnomad4 AMR
AF:
0.516
Gnomad4 ASJ
AF:
0.410
Gnomad4 EAS
AF:
0.527
Gnomad4 SAS
AF:
0.567
Gnomad4 FIN
AF:
0.482
Gnomad4 NFE
AF:
0.441
Gnomad4 OTH
AF:
0.548
Alfa
AF:
0.468
Hom.:
22909
Bravo
AF:
0.582
Asia WGS
AF:
0.555
AC:
1928
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
2.8
DANN
Benign
0.42

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9853939; hg19: chr3-31989487; API