rs4758533

chr11-3128856-A-G

Variant summary

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

The NM_020896.4(OSBPL5):c.136+157T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 152,140 control chromosomes in the GnomAD database, including 49,075 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 0.80 (49075 hom., cov: 33)
• Consequence: OSBPL5 NM_020896.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.28

Genes affected

OSBPL5 (HGNC:16392): (oxysterol binding protein like 5) This gene encodes a member of the oxysterol-binding protein (OSBP) family, a group of intracellular lipid receptors that play a key role in the maintenance of cholesterol balance in the body. Most members contain an N-terminal pleckstrin homology domain and a highly conserved C-terminal OSBP-like sterol-binding domain. This gene has been shown to be imprinted, with preferential expression from the maternal allele only in placenta. Transcript variants encoding different isoforms have been identified. [provided by RefSeq, Oct 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL5	NM_020896.4	c.136+157T>C		intron_variant		ENST00000263650.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL5	ENST00000263650.12	c.136+157T>C		intron_variant		1	NM_020896.4	P1

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121327 AN: 152022 Hom.: 49036 Cov.: 33

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.798 AC: 121417 AN: 152140 Hom.: 49075 Cov.: 33 AF XY: 0.794 AC XY: 59091 AN XY: 74378

Gnomad4 AFR AF: 0.889

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.879

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.748

Alfa AF: 0.779 Hom.: 56947

Bravo AF: 0.792

Asia WGS AF: 0.585 AC: 2036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.073
Dann	Benign	0.39

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: rs4758533; hg19: chr11-3150086;