chr7-24973080-G-A

Position:

• chr7-24973080-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015550.4(OSBPL3):​c.-150+6806C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,946 control chromosomes in the GnomAD database, including 7,741 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 0.32 (7741 hom., cov: 32)
• Consequence: OSBPL3 NM_015550.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OSBPL3	NM_015550.4	c.-150+6806C>T		intron_variant		ENST00000313367.7	NP_056365.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OSBPL3	ENST00000313367.7	c.-150+6806C>T		intron_variant		1	NM_015550.4	ENSP00000315410	P3
OSBPL3	ENST00000415952.1	c.-150+8319C>T		intron_variant		4		ENSP00000411249

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47892 AN: 151828 Hom.: 7741 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.315 AC: 47912 AN: 151946 Hom.: 7741 Cov.: 32 AF XY: 0.316 AC XY: 23490 AN XY: 74270

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.315

Alfa AF: 0.289 Hom.: 10164

Bravo AF: 0.327

Asia WGS AF: 0.245 AC: 852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.6
DANN	Benign	0.59

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

Publications

LitVar

Other links and lift over

dbSNP: rs149; hg19: chr7-25012699;