NM_015550.4:c.-150+1543G>A

Variant names:

• chr7-24978343-C-T
• rs158
• NM_015550.4:c.-150+1543G>A

Variant summary

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

The NM_015550.4(OSBPL3):​c.-150+1543G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.852 in 152,302 control chromosomes in the GnomAD database, including 55,659 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 0.85 (55659 hom., cov: 34)
• Consequence: OSBPL3 NM_015550.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL3	NM_015550.4	c.-150+1543G>A		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.-150+1543G>A		intron_variant	Intron 1 of 22	1	NM_015550.4	ENSP00000315410.2
OSBPL3	ENST00000415952.1	c.-150+3056G>A		intron_variant	Intron 1 of 2	4		ENSP00000411249.1

Frequencies

GnomAD3 genomes AF: 0.852 AC: 129598 AN: 152184 Hom.: 55592 Cov.: 34

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.852 AC: 129725 AN: 152302 Hom.: 55659 Cov.: 34 AF XY: 0.854 AC XY: 63568 AN XY: 74472

African (AFR) AF: 0.949 AC: 39457 AN: 41582

American (AMR) AF: 0.872 AC: 13350 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2770 AN: 3472

East Asian (EAS) AF: 0.835 AC: 4336 AN: 5192

South Asian (SAS) AF: 0.916 AC: 4422 AN: 4830

European-Finnish (FIN) AF: 0.769 AC: 8144 AN: 10590

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.802 AC: 54519 AN: 68014

Other (OTH) AF: 0.859 AC: 1816 AN: 2114

Alfa AF: 0.828 Hom.: 19491

Bravo AF: 0.861

Asia WGS AF: 0.881 AC: 3067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.049
DANN	Benign	0.43
PhyloP100		-1.6
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: rs158; hg19: chr7-25017962;