rs10862080

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020841.5(OSBPL8):​c.-68+24202A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,046 control chromosomes in the GnomAD database, including 1,278 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 0.11 ( 1278 hom., cov: 32)

Consequence

OSBPL8
NM_020841.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.515
Variant links:
Genes affected
OSBPL8 (HGNC:16396): (oxysterol binding protein like 8) This gene encodes a member of a family of proteins containing an N-terminal pleckstrin homology domain and a highly conserved C-terminal oxysterol-binding protein-like sterol-binding domain. It binds mutliple lipid-containing molecules, including phosphatidylserine, phosphatidylinositol 4-phosphate (PI4P) and oxysterol, and promotes their exchange between the endoplasmic reticulum and the plasma membrane. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OSBPL8NM_020841.5 linkuse as main transcriptc.-68+24202A>T intron_variant ENST00000261183.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OSBPL8ENST00000261183.8 linkuse as main transcriptc.-68+24202A>T intron_variant 1 NM_020841.5 P3Q9BZF1-1

Frequencies

GnomAD3 genomes
AF:
0.107
AC:
16186
AN:
151928
Hom.:
1274
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0231
Gnomad AMI
AF:
0.0746
Gnomad AMR
AF:
0.121
Gnomad ASJ
AF:
0.144
Gnomad EAS
AF:
0.363
Gnomad SAS
AF:
0.198
Gnomad FIN
AF:
0.182
Gnomad MID
AF:
0.140
Gnomad NFE
AF:
0.114
Gnomad OTH
AF:
0.119
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.107
AC:
16198
AN:
152046
Hom.:
1278
Cov.:
32
AF XY:
0.114
AC XY:
8451
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.0231
Gnomad4 AMR
AF:
0.121
Gnomad4 ASJ
AF:
0.144
Gnomad4 EAS
AF:
0.362
Gnomad4 SAS
AF:
0.199
Gnomad4 FIN
AF:
0.182
Gnomad4 NFE
AF:
0.114
Gnomad4 OTH
AF:
0.128
Alfa
AF:
0.109
Hom.:
124
Bravo
AF:
0.0959
Asia WGS
AF:
0.275
AC:
946
AN:
3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.67
DANN
Benign
0.25

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: rs10862080; hg19: chr12-76928975; API