rs17178177

chr11-3087641-C-G

Variant summary

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

The NM_020896.4(OSBPL5):c.*564G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,930 control chromosomes in the GnomAD database, including 875 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 0.10 (870 hom., cov: 33)
  • Exomes 𝑓: 0.11 (5 hom.)
• Consequence: OSBPL5 NM_020896.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.440

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL5	NM_020896.4	c.*564G>C		3_prime_UTR_variant	22/22	ENST00000263650.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL5	ENST00000263650.12	c.*564G>C		3_prime_UTR_variant	22/22	1	NM_020896.4	P1

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15371 AN: 152042 Hom.: 871 Cov.: 33

Gnomad AFR AF: 0.0990

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.0686

Gnomad ASJ AF: 0.0593

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0892

Gnomad FIN AF: 0.0961

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0932

GnomAD4 exome AF: 0.106 AC: 82 AN: 774 Hom.: 5 Cov.: 0 AF XY: 0.116 AC XY: 54 AN XY: 464

Gnomad4 AFR exome AF: 0.0625

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.135

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.109

Gnomad4 OTH exome AF: 0.148

GnomAD4 genome AF: 0.101 AC: 15373 AN: 152156 Hom.: 870 Cov.: 33 AF XY: 0.0983 AC XY: 7316 AN XY: 74406

Gnomad4 AFR AF: 0.0990

Gnomad4 AMR AF: 0.0686

Gnomad4 ASJ AF: 0.0593

Gnomad4 EAS AF: 0.00290

Gnomad4 SAS AF: 0.0892

Gnomad4 FIN AF: 0.0961

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.0908

Alfa AF: 0.109 Hom.: 116

Bravo AF: 0.0986

Asia WGS AF: 0.0420 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	5.5
Dann	Benign	0.49

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: rs17178177; hg19: chr11-3108871;