NM_015550.4:c.-149-34206G>T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015550.4(OSBPL3):c.-149-34206G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 152,082 control chromosomes in the GnomAD database, including 26,856 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 0.58 ( 26856 hom., cov: 33)
Consequence
OSBPL3
NM_015550.4 intron
NM_015550.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.644
Publications
7 publications found
Genes affected
OSBPL3 (HGNC:16370): (oxysterol binding protein like 3) 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. The encoded protein is involved in the regulation of cell adhesion and organization of the actin cytoskeleton. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.584 AC: 88672AN: 151964Hom.: 26844 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
88672
AN:
151964
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.583 AC: 88728AN: 152082Hom.: 26856 Cov.: 33 AF XY: 0.589 AC XY: 43766AN XY: 74330 show subpopulations
GnomAD4 genome
AF:
AC:
88728
AN:
152082
Hom.:
Cov.:
33
AF XY:
AC XY:
43766
AN XY:
74330
show subpopulations
African (AFR)
AF:
AC:
29164
AN:
41472
American (AMR)
AF:
AC:
9007
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
AC:
1906
AN:
3470
East Asian (EAS)
AF:
AC:
4696
AN:
5170
South Asian (SAS)
AF:
AC:
3434
AN:
4818
European-Finnish (FIN)
AF:
AC:
5448
AN:
10564
Middle Eastern (MID)
AF:
AC:
140
AN:
294
European-Non Finnish (NFE)
AF:
AC:
33283
AN:
67986
Other (OTH)
AF:
AC:
1132
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1860
3721
5581
7442
9302
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
738
1476
2214
2952
3690
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2709
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.