7-24918662-C-T

Variant names:

• chr7-24918662-C-T
• rs129
• NM_015550.4:c.-149-26041G>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.-149-26041G>A 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 152,082 control chromosomes in the GnomAD database, including 32,984 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 (32984 hom., cov: 33)
• Consequence: OSBPL3 NM_015550.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 3 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015550.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL3	NM_015550.4	MANE Select	c.-149-26041G>A		intron	N/A	NP_056365.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL3	ENST00000313367.7	TSL:1 MANE Select	c.-149-26041G>A		intron	N/A	ENSP00000315410.2
	OSBPL3	ENST00000415952.1	TSL:4	c.-149-26041G>A		intron	N/A	ENSP00000411249.1

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98142 AN: 151964 Hom.: 32944 Cov.: 33

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.646 AC: 98240 AN: 152082 Hom.: 32984 Cov.: 33 AF XY: 0.649 AC XY: 48226 AN XY: 74336

African (AFR) AF: 0.809 AC: 33594 AN: 41510

American (AMR) AF: 0.636 AC: 9717 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2083 AN: 3472

East Asian (EAS) AF: 0.908 AC: 4709 AN: 5188

South Asian (SAS) AF: 0.728 AC: 3507 AN: 4816

European-Finnish (FIN) AF: 0.550 AC: 5801 AN: 10550

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36760 AN: 67960

Other (OTH) AF: 0.603 AC: 1269 AN: 2106

Alfa AF: 0.575 Hom.: 12987

Bravo AF: 0.654

Asia WGS AF: 0.820 AC: 2850 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.55
DANN	Benign	0.43
PhyloP100		0.078
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: rs129; hg19: chr7-24958281;