rs6803685

Variant names:

• chr3-31708233-C-T
• rs6803685
• NM_017784.5:c.1096-5725G>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.1096-5725G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 152,072 control chromosomes in the GnomAD database, including 31,784 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 0.64 (31784 hom., cov: 32)
• Consequence: OSBPL10 NM_017784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 1 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]

OSBPL10-AS1 (HGNC:40767): (OSBPL10 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.719 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.1096-5725G>A		intron	N/A	NP_060254.2
	OSBPL10	NM_001174060.2		c.904-5725G>A		intron	N/A	NP_001167531.1	Q9BXB5-2
	OSBPL10-AS1	NR_049771.1		n.28-2705C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL10	ENST00000396556.7	TSL:1 MANE Select	c.1096-5725G>A		intron	N/A	ENSP00000379804.2	Q9BXB5-1
	OSBPL10	ENST00000959571.1		c.991-5725G>A		intron	N/A	ENSP00000629630.1
	OSBPL10	ENST00000911816.1		c.1096-24119G>A		intron	N/A	ENSP00000581875.1

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96933 AN: 151952 Hom.: 31763 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.638 AC: 96989 AN: 152072 Hom.: 31784 Cov.: 32 AF XY: 0.631 AC XY: 46866 AN XY: 74318

African (AFR) AF: 0.551 AC: 22836 AN: 41438

American (AMR) AF: 0.519 AC: 7929 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2374 AN: 3468

East Asian (EAS) AF: 0.345 AC: 1789 AN: 5178

South Asian (SAS) AF: 0.622 AC: 2996 AN: 4820

European-Finnish (FIN) AF: 0.727 AC: 7688 AN: 10570

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.724 AC: 49248 AN: 67994

Other (OTH) AF: 0.645 AC: 1362 AN: 2110

Alfa AF: 0.687 Hom.: 4553

Bravo AF: 0.615

Asia WGS AF: 0.530 AC: 1846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.39
PhyloP100		-1.8
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: rs6803685; hg19: chr3-31749725;