rs9878129

chr3-31970578-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017784.5(OSBPL10):c.281+10321G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 152,118 control chromosomes in the GnomAD database, including 15,446 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 0.41 (15446 hom., cov: 32)
• Consequence: OSBPL10 NM_017784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.802

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL10	NM_017784.5	c.281+10321G>A		intron_variant		ENST00000396556.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL10	ENST00000396556.7	c.281+10321G>A		intron_variant		1	NM_017784.5	P2

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62732 AN: 152000 Hom.: 15403 Cov.: 32

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.378

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.413 AC: 62829 AN: 152118 Hom.: 15446 Cov.: 32 AF XY: 0.422 AC XY: 31369 AN XY: 74346

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.764

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.385

Alfa AF: 0.369 Hom.: 2262

Bravo AF: 0.429

Asia WGS AF: 0.692 AC: 2403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.19
Dann	Benign	0.26

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

Other links and lift over

dbSNP: rs9878129; hg19: chr3-32012070;