chr3-31926475-G-A

Position:

• chr3-31926475-G-A

Variant summary

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

The NM_017784.5(OSBPL10):​c.282-46645C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,002 control chromosomes in the GnomAD database, including 4,328 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 (4328 hom., cov: 31)
• Consequence: OSBPL10 NM_017784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OSBPL10	NM_017784.5	c.282-46645C>T		intron_variant		ENST00000396556.7	NP_060254.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OSBPL10	ENST00000396556.7	c.282-46645C>T		intron_variant		1	NM_017784.5	ENSP00000379804.2

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35733 AN: 151884 Hom.: 4331 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.235 AC: 35732 AN: 152002 Hom.: 4328 Cov.: 31 AF XY: 0.227 AC XY: 16873 AN XY: 74288

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.256

Alfa AF: 0.254 Hom.: 1456

Bravo AF: 0.234

Asia WGS AF: 0.203 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.1
DANN	Benign	0.95

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: rs6810295; hg19: chr3-31967967;