rs9878129

Variant names:

• chr3-31970578-C-T
• rs9878129
• NM_017784.5:c.281+10321G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017784.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL10	NM_017784.5	MANE Select	c.281+10321G>A		intron	N/A	NP_060254.2
	OSBPL10	NM_001174060.2		c.281+10321G>A		intron	N/A	NP_001167531.1	Q9BXB5-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL10	ENST00000396556.7	TSL:1 MANE Select	c.281+10321G>A		intron	N/A	ENSP00000379804.2	Q9BXB5-1
	OSBPL10	ENST00000959571.1		c.281+10321G>A		intron	N/A	ENSP00000629630.1
	OSBPL10	ENST00000911816.1		c.281+10321G>A		intron	N/A	ENSP00000581875.1

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

African (AFR) AF: 0.640 AC: 26573 AN: 41494

American (AMR) AF: 0.426 AC: 6519 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 892 AN: 3470

East Asian (EAS) AF: 0.764 AC: 3930 AN: 5144

South Asian (SAS) AF: 0.538 AC: 2596 AN: 4824

European-Finnish (FIN) AF: 0.346 AC: 3656 AN: 10576

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.257 AC: 17470 AN: 68008

Other (OTH) AF: 0.385 AC: 813 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.19
DANN	Benign	0.26
PhyloP100		-0.80
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9878129; hg19: chr3-32012070;