NM_015550.4:c.-149-34206G>T

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.644

Publications

7 publications found
Variant links:
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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OSBPL3NM_015550.4 linkc.-149-34206G>T intron_variant Intron 1 of 22 ENST00000313367.7 NP_056365.1 Q9H4L5-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OSBPL3ENST00000313367.7 linkc.-149-34206G>T intron_variant Intron 1 of 22 1 NM_015550.4 ENSP00000315410.2 Q9H4L5-1
OSBPL3ENST00000415952.1 linkc.-149-34206G>T intron_variant Intron 1 of 2 4 ENSP00000411249.1 C9J8P4

Frequencies

GnomAD3 genomes
AF:
0.584
AC:
88672
AN:
151964
Hom.:
26844
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.704
Gnomad AMI
AF:
0.569
Gnomad AMR
AF:
0.589
Gnomad ASJ
AF:
0.549
Gnomad EAS
AF:
0.909
Gnomad SAS
AF:
0.712
Gnomad FIN
AF:
0.516
Gnomad MID
AF:
0.487
Gnomad NFE
AF:
0.490
Gnomad OTH
AF:
0.537
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.583
AC:
88728
AN:
152082
Hom.:
26856
Cov.:
33
AF XY:
0.589
AC XY:
43766
AN XY:
74330
show subpopulations
African (AFR)
AF:
0.703
AC:
29164
AN:
41472
American (AMR)
AF:
0.589
AC:
9007
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.549
AC:
1906
AN:
3470
East Asian (EAS)
AF:
0.908
AC:
4696
AN:
5170
South Asian (SAS)
AF:
0.713
AC:
3434
AN:
4818
European-Finnish (FIN)
AF:
0.516
AC:
5448
AN:
10564
Middle Eastern (MID)
AF:
0.476
AC:
140
AN:
294
European-Non Finnish (NFE)
AF:
0.490
AC:
33283
AN:
67986
Other (OTH)
AF:
0.535
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:
0.521
Hom.:
81482
Bravo
AF:
0.589
Asia WGS
AF:
0.779
AC:
2709
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
4.7
DANN
Benign
0.46
PhyloP100
0.64
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs123; hg19: chr7-24966446; API