NM_015550.4:c.-149-34206G>T

Variant names:

• chr7-24926827-C-A
• rs123
• NM_015550.4:c.-149-34206G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015550.4(OSBPL3):​c.-149-34206G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 152,082 control chromosomes in the GnomAD database, including 26,856 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 0.58 (26856 hom., cov: 33)
• Consequence: OSBPL3 NM_015550.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.644
• Publications: 7 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL3	NM_015550.4	c.-149-34206G>T		intron_variant	Intron 1 of 22	ENST00000313367.7	NP_056365.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSBPL3	ENST00000313367.7	c.-149-34206G>T		intron_variant	Intron 1 of 22	1	NM_015550.4	ENSP00000315410.2
OSBPL3	ENST00000415952.1	c.-149-34206G>T		intron_variant	Intron 1 of 2	4		ENSP00000411249.1

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88672 AN: 151964 Hom.: 26844 Cov.: 33

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.583 AC: 88728 AN: 152082 Hom.: 26856 Cov.: 33 AF XY: 0.589 AC XY: 43766 AN XY: 74330

African (AFR) AF: 0.703 AC: 29164 AN: 41472

American (AMR) AF: 0.589 AC: 9007 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1906 AN: 3470

East Asian (EAS) AF: 0.908 AC: 4696 AN: 5170

South Asian (SAS) AF: 0.713 AC: 3434 AN: 4818

European-Finnish (FIN) AF: 0.516 AC: 5448 AN: 10564

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33283 AN: 67986

Other (OTH) AF: 0.535 AC: 1132 AN: 2114

Alfa AF: 0.521 Hom.: 81482

Bravo AF: 0.589

Asia WGS AF: 0.779 AC: 2709 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	4.7
DANN	Benign	0.46
PhyloP100		0.64
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs123; hg19: chr7-24966446;