NM_015550.4:c.-149-25802T>C

Variant names:

• chr7-24918423-A-G
• rs120
• NM_015550.4:c.-149-25802T>C

Variant summary

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

The NM_015550.4(OSBPL3):​c.-149-25802T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 152,086 control chromosomes in the GnomAD database, including 32,987 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 0.65 (32987 hom., cov: 32)
• Consequence: OSBPL3 NM_015550.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305
• Publications: 12 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 (EAS) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL3	NM_015550.4	c.-149-25802T>C		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.-149-25802T>C		intron_variant	Intron 1 of 22	1	NM_015550.4	ENSP00000315410.2
OSBPL3	ENST00000415952.1	c.-149-25802T>C		intron_variant	Intron 1 of 2	4		ENSP00000411249.1

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98132 AN: 151968 Hom.: 32947 Cov.: 32

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.646 AC: 98230 AN: 152086 Hom.: 32987 Cov.: 32 AF XY: 0.649 AC XY: 48208 AN XY: 74314

African (AFR) AF: 0.809 AC: 33599 AN: 41518

American (AMR) AF: 0.636 AC: 9708 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2083 AN: 3470

East Asian (EAS) AF: 0.907 AC: 4697 AN: 5176

South Asian (SAS) AF: 0.728 AC: 3512 AN: 4826

European-Finnish (FIN) AF: 0.549 AC: 5801 AN: 10562

Middle Eastern (MID) AF: 0.558 AC: 163 AN: 292

European-Non Finnish (NFE) AF: 0.541 AC: 36765 AN: 67968

Other (OTH) AF: 0.601 AC: 1266 AN: 2106

Alfa AF: 0.601 Hom.: 9465

Bravo AF: 0.654

Asia WGS AF: 0.821 AC: 2856 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	1.0
DANN	Benign	0.52
PhyloP100		-0.30
PromoterAI		0.015	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs120; hg19: chr7-24958042;