chr7-24943836-C-T

Variant names:

• chr7-24943836-C-T
• rs2710994
• NM_015550.4:c.-150+36050G>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+36050G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,968 control chromosomes in the GnomAD database, including 7,960 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 0.28 (7960 hom., cov: 32)
• Consequence: OSBPL3 NM_015550.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 8 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.763 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL3	NM_015550.4	MANE Select	c.-150+36050G>A		intron	N/A	NP_056365.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL3	ENST00000313367.7	TSL:1 MANE Select	c.-150+36050G>A		intron	N/A	ENSP00000315410.2
	OSBPL3	ENST00000969022.1		c.-150+36050G>A		intron	N/A	ENSP00000639081.1
	OSBPL3	ENST00000940424.1		c.-150+36050G>A		intron	N/A	ENSP00000610483.1

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43015 AN: 151848 Hom.: 7937 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.284 AC: 43092 AN: 151968 Hom.: 7960 Cov.: 32 AF XY: 0.292 AC XY: 21691 AN XY: 74276

African (AFR) AF: 0.415 AC: 17181 AN: 41440

American (AMR) AF: 0.269 AC: 4106 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3470

East Asian (EAS) AF: 0.783 AC: 4052 AN: 5176

South Asian (SAS) AF: 0.589 AC: 2836 AN: 4812

European-Finnish (FIN) AF: 0.180 AC: 1897 AN: 10548

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11579 AN: 67940

Other (OTH) AF: 0.251 AC: 529 AN: 2104

Alfa AF: 0.198 Hom.: 6158

Bravo AF: 0.292

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.7
DANN	Benign	0.62
PhyloP100		-0.056
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: rs2710994; hg19: chr7-24983455;