rs757139

chr7-24939736-A-Cchr7-24939736-A-T

Variant summary

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

The NM_015550.4(OSBPL3):c.-150+40150T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 151,924 control chromosomes in the GnomAD database, including 14,567 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 0.43 (14567 hom., cov: 31)
• Consequence: OSBPL3 NM_015550.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.876

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL3	NM_015550.4	c.-150+40150T>G		intron_variant		ENST00000313367.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL3	ENST00000313367.7	c.-150+40150T>G		intron_variant		1	NM_015550.4	P3
OSBPL3	ENST00000415952.1	c.-150+41663T>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.428 AC: 65030 AN: 151806 Hom.: 14571 Cov.: 31

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.428 AC: 65055 AN: 151924 Hom.: 14567 Cov.: 31 AF XY: 0.428 AC XY: 31772 AN XY: 74236

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.549

Gnomad4 SAS AF: 0.629

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.435

Alfa AF: 0.473 Hom.: 22116

Bravo AF: 0.424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.68
Dann	Benign	0.73
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs757139; hg19: chr7-24979355;