chr1-51760724-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_024586.6(OSBPL9):c.617C>T(p.Pro206Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000235 in 1,613,842 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00024 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00023 ( 0 hom. )
Consequence
OSBPL9
NM_024586.6 missense
NM_024586.6 missense
Scores
1
6
10
Clinical Significance
Conservation
PhyloP100: 6.46
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.12636927).
BS2
?
High AC in GnomAd at 37 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OSBPL9 | NM_024586.6 | c.617C>T | p.Pro206Leu | missense_variant | 10/24 | ENST00000428468.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OSBPL9 | ENST00000428468.6 | c.617C>T | p.Pro206Leu | missense_variant | 10/24 | 1 | NM_024586.6 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000243 AC: 37AN: 152140Hom.: 0 Cov.: 32
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?
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GnomAD3 exomes AF: 0.000115 AC: 29AN: 251330Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135828
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GnomAD4 exome AF: 0.000235 AC: 343AN: 1461584Hom.: 0 Cov.: 30 AF XY: 0.000198 AC XY: 144AN XY: 727106
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GnomAD4 genome ? AF: 0.000243 AC: 37AN: 152258Hom.: 0 Cov.: 32 AF XY: 0.000309 AC XY: 23AN XY: 74438
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 01, 2022 | The c.647C>T (p.P216L) alteration is located in exon 10 (coding exon 10) of the OSBPL9 gene. This alteration results from a C to T substitution at nucleotide position 647, causing the proline (P) at amino acid position 216 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
Cadd
Pathogenic
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;D;D;D;D;.;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D;D;D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;D;D;N;N;N;N
REVEL
Benign
Sift
Benign
T;T;D;D;D;D;D;T;D;D
Sift4G
Benign
T;T;T;T;D;D;T;T;T;T
Polyphen
0.97, 0.99
.;.;D;.;.;.;.;D;.;.
Vest4
MVP
MPC
0.41
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at