rs10486445

chr7-24974363-A-G

Variant summary

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

The NM_015550.4(OSBPL3):c.-150+5523T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 152,178 control chromosomes in the GnomAD database, including 7,320 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 0.29 (7320 hom., cov: 33)
• Consequence: OSBPL3 NM_015550.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.341

Genes affected

OSBPL3 (HGNC:16370): (oxysterol binding protein like 3) This gene encodes a member of the oxysterol-binding protein (OSBP) family, a group of intracellular lipid receptors. Most members contain an N-terminal pleckstrin homology domain and a highly conserved C-terminal OSBP-like sterol-binding domain. The encoded protein is involved in the regulation of cell adhesion and organization of the actin cytoskeleton. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL3	NM_015550.4	c.-150+5523T>C		intron_variant		ENST00000313367.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL3	ENST00000313367.7	c.-150+5523T>C		intron_variant		1	NM_015550.4	P3
OSBPL3	ENST00000415952.1	c.-150+7036T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44586 AN: 152060 Hom.: 7323 Cov.: 33

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.0127

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.293 AC: 44589 AN: 152178 Hom.: 7320 Cov.: 33 AF XY: 0.284 AC XY: 21159 AN XY: 74394

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.0127

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.317

Alfa AF: 0.363 Hom.: 14406

Bravo AF: 0.282

Asia WGS AF: 0.125 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	3.9
Dann	Benign	0.48

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: rs10486445; hg19: chr7-25013982;