rs1053746

chr11-3087455-G-Achr11-3087455-G-T

Variant summary

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

The NM_020896.4(OSBPL5):c.*750C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0415 in 154,368 control chromosomes in the GnomAD database, including 167 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 0.042 (165 hom., cov: 33)
  • Exomes 𝑓: 0.029 (2 hom.)
• Consequence: OSBPL5 NM_020896.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL5	NM_020896.4	c.*750C>T		3_prime_UTR_variant	22/22	ENST00000263650.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL5	ENST00000263650.12	c.*750C>T		3_prime_UTR_variant	22/22	1	NM_020896.4	P1
OSBPL5	ENST00000389989.7	c.*750C>T		3_prime_UTR_variant	21/21	1
OSBPL5	ENST00000478260.5	c.*750C>T		3_prime_UTR_variant	8/8	2
OSBPL5	ENST00000534454.5	c.*356C>T		3_prime_UTR_variant	12/12	5

Frequencies

GnomAD3 genomes AF: 0.0416 AC: 6329 AN: 152076 Hom.: 165 Cov.: 33

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0180

Gnomad ASJ AF: 0.0531

Gnomad EAS AF: 0.00290

Gnomad SAS AF: 0.0705

Gnomad FIN AF: 0.0382

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0299

Gnomad OTH AF: 0.0288

GnomAD4 exome AF: 0.0290 AC: 63 AN: 2174 Hom.: 2 Cov.: 0 AF XY: 0.0335 AC XY: 37 AN XY: 1104

Gnomad4 AFR exome AF: 0.0286

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0938

Gnomad4 FIN exome AF: 0.0556

Gnomad4 NFE exome AF: 0.0120

Gnomad4 OTH exome AF: 0.0536

GnomAD4 genome AF: 0.0417 AC: 6342 AN: 152194 Hom.: 165 Cov.: 33 AF XY: 0.0418 AC XY: 3111 AN XY: 74408

Gnomad4 AFR AF: 0.0695

Gnomad4 AMR AF: 0.0179

Gnomad4 ASJ AF: 0.0531

Gnomad4 EAS AF: 0.00291

Gnomad4 SAS AF: 0.0706

Gnomad4 FIN AF: 0.0382

Gnomad4 NFE AF: 0.0299

Gnomad4 OTH AF: 0.0318

Alfa AF: 0.0305 Hom.: 71

Bravo AF: 0.0396

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.037
Dann	Benign	0.78

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: rs1053746; hg19: chr11-3108685;