rs12171283
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_017784.5(OSBPL10):c.730-32725G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.37 ( 1188 hom., cov: 0)
Failed GnomAD Quality Control
Consequence
OSBPL10
NM_017784.5 intron
NM_017784.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.14
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 Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OSBPL10 | NM_017784.5 | c.730-32725G>T | intron_variant | ENST00000396556.7 | NP_060254.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OSBPL10 | ENST00000396556.7 | c.730-32725G>T | intron_variant | 1 | NM_017784.5 | ENSP00000379804.2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 12987AN: 34728Hom.: 1172 Cov.: 0 FAILED QC
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.375 AC: 13044AN: 34822Hom.: 1188 Cov.: 0 AF XY: 0.376 AC XY: 6321AN XY: 16804
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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