rs3792551

chr3-31665408-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.2097-1176C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,166 control chromosomes in the GnomAD database, including 1,115 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 0.10 (1115 hom., cov: 32)
• Consequence: OSBPL10 NM_017784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.525

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL10	NM_017784.5	c.2097-1176C>T		intron_variant		ENST00000396556.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL10	ENST00000396556.7	c.2097-1176C>T		intron_variant		1	NM_017784.5	P2
OSBPL10	ENST00000429492.6	c.1403-1176C>T		intron_variant		2
OSBPL10	ENST00000438237.6	c.1905-1176C>T		intron_variant		2		A2

Frequencies

GnomAD3 genomes AF: 0.0998 AC: 15167 AN: 152048 Hom.: 1104 Cov.: 32

Gnomad AFR AF: 0.0697

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.0838

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0732

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.100 AC: 15216 AN: 152166 Hom.: 1115 Cov.: 32 AF XY: 0.107 AC XY: 7928 AN XY: 74398

Gnomad4 AFR AF: 0.0697

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.0838

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.0732

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0891 Hom.: 1219

Bravo AF: 0.110

Asia WGS AF: 0.209 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.7
Dann	Benign	0.74

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: rs3792551; hg19: chr3-31706900;