1-51746715-T-G

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2

The NM_001330580.2(OSBPL9):​c.-76T>G variant causes a 5 prime UTR premature start codon gain change. The variant allele was found at a frequency of 0.000427 in 1,608,382 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00022 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00045 ( 1 hom. )

Consequence

OSBPL9
NM_001330580.2 5_prime_UTR_premature_start_codon_gain

Scores

2
3
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.01
Variant links:
Genes affected
OSBPL9 (HGNC:16386): (oxysterol binding protein like 9) 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, although some members contain only the sterol-binding domain. This family member functions as a cholesterol transfer protein that regulates Golgi structure and function. Multiple transcript variants, most of which encode distinct isoforms, have been identified. Related pseudogenes have been identified on chromosomes 3, 11 and 12. [provided by RefSeq, Jul 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.27594197).
BS2
High AC in GnomAd4 at 34 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OSBPL9NM_024586.6 linkc.420T>G p.Phe140Leu missense_variant Exon 6 of 24 ENST00000428468.6 NP_078862.4 Q96SU4-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OSBPL9ENST00000428468.6 linkc.420T>G p.Phe140Leu missense_variant Exon 6 of 24 1 NM_024586.6 ENSP00000407168.1 Q96SU4-1

Frequencies

GnomAD3 genomes
AF:
0.000223
AC:
34
AN:
152226
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000724
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000196
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000412
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000173
AC:
43
AN:
248420
Hom.:
1
AF XY:
0.000186
AC XY:
25
AN XY:
134274
show subpopulations
Gnomad AFR exome
AF:
0.000124
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000363
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000448
AC:
652
AN:
1456156
Hom.:
1
Cov.:
29
AF XY:
0.000424
AC XY:
307
AN XY:
724558
show subpopulations
Gnomad4 AFR exome
AF:
0.0000602
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.0000384
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000187
Gnomad4 NFE exome
AF:
0.000541
Gnomad4 OTH exome
AF:
0.000798
GnomAD4 genome
AF:
0.000223
AC:
34
AN:
152226
Hom.:
0
Cov.:
32
AF XY:
0.000242
AC XY:
18
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.0000724
Gnomad4 AMR
AF:
0.000196
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000412
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000285
Hom.:
0
Bravo
AF:
0.000189
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000698
AC:
6
ExAC
AF:
0.000124
AC:
15
EpiCase
AF:
0.000383
EpiControl
AF:
0.0000593

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Oct 19, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.489T>G (p.F163L) alteration is located in exon 7 (coding exon 7) of the OSBPL9 gene. This alteration results from a T to G substitution at nucleotide position 489, causing the phenylalanine (F) at amino acid position 163 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.79
BayesDel_addAF
Benign
-0.21
T
BayesDel_noAF
Benign
-0.21
CADD
Uncertain
25
DANN
Uncertain
0.99
DEOGEN2
Benign
0.015
.;.;T;.;.
Eigen
Benign
0.10
Eigen_PC
Benign
0.18
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Uncertain
0.87
D;D;D;D;D
M_CAP
Benign
0.0072
T
MetaRNN
Benign
0.28
T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.3
L;.;L;.;.
PrimateAI
Pathogenic
0.86
D
PROVEAN
Benign
0.38
N;N;N;N;N
REVEL
Benign
0.19
Sift
Benign
1.0
T;T;T;T;T
Sift4G
Benign
1.0
T;T;T;T;T
Polyphen
0.99, 0.99
.;.;D;.;D
Vest4
0.72
MVP
0.45
MPC
0.11
ClinPred
0.098
T
GERP RS
4.7
Varity_R
0.26
gMVP
0.37

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: rs148909045; hg19: chr1-52212387; API