rs4758538

Variant names:

• chr11-3141164-C-T
• rs4758538
• NM_020896.4:c.-21-11995G>A

Variant summary

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

The NM_020896.4(OSBPL5):​c.-21-11995G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,010 control chromosomes in the GnomAD database, including 6,596 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 (6596 hom., cov: 32)
• Consequence: OSBPL5 NM_020896.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL5	NM_020896.4	c.-21-11995G>A		intron_variant	Intron 1 of 21	ENST00000263650.12	NP_065947.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSBPL5	ENST00000263650.12	c.-21-11995G>A		intron_variant	Intron 1 of 21	1	NM_020896.4	ENSP00000263650.7

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43023 AN: 151892 Hom.: 6581 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.283 AC: 43078 AN: 152010 Hom.: 6596 Cov.: 32 AF XY: 0.283 AC XY: 21006 AN XY: 74296

African (AFR) AF: 0.412 AC: 17070 AN: 41420

American (AMR) AF: 0.251 AC: 3841 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 870 AN: 3464

East Asian (EAS) AF: 0.194 AC: 1002 AN: 5156

South Asian (SAS) AF: 0.254 AC: 1226 AN: 4820

European-Finnish (FIN) AF: 0.225 AC: 2382 AN: 10580

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15823 AN: 67978

Other (OTH) AF: 0.267 AC: 564 AN: 2110

Alfa AF: 0.256 Hom.: 3359

Bravo AF: 0.292

Asia WGS AF: 0.232 AC: 811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.34
PhyloP100		-0.68
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs4758538; hg19: chr11-3162394;