3-31766084-C-T

Variant names:

• chr3-31766084-C-T
• rs11716163
• NM_017784.5:c.730-17964G>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.730-17964G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,008 control chromosomes in the GnomAD database, including 5,933 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 0.24 (5933 hom., cov: 31)
• Consequence: OSBPL10 NM_017784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.548 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.730-17964G>A		intron	N/A	NP_060254.2
	OSBPL10	NM_001174060.2		c.538-17964G>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.730-17964G>A		intron	N/A	ENSP00000379804.2	Q9BXB5-1
	OSBPL10	ENST00000959571.1		c.625-17964G>A		intron	N/A	ENSP00000629630.1
	OSBPL10	ENST00000911816.1		c.730-17964G>A		intron	N/A	ENSP00000581875.1

Frequencies

GnomAD3 genomes AF: 0.244 AC: 36991 AN: 151890 Hom.: 5933 Cov.: 31

Gnomad AFR AF: 0.0545

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.243 AC: 36987 AN: 152008 Hom.: 5933 Cov.: 31 AF XY: 0.248 AC XY: 18415 AN XY: 74292

African (AFR) AF: 0.0543 AC: 2254 AN: 41502

American (AMR) AF: 0.394 AC: 6016 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1069 AN: 3462

East Asian (EAS) AF: 0.565 AC: 2909 AN: 5148

South Asian (SAS) AF: 0.368 AC: 1768 AN: 4808

European-Finnish (FIN) AF: 0.253 AC: 2665 AN: 10554

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19493 AN: 67966

Other (OTH) AF: 0.254 AC: 536 AN: 2110

Alfa AF: 0.274 Hom.: 10570

Bravo AF: 0.243

Asia WGS AF: 0.388 AC: 1350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.98
DANN	Benign	0.72
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs11716163; hg19: chr3-31807576;