rs8813

Positions:

• chr11-3087276-G-A

Variant summary

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

The NM_020896.4(OSBPL5):​c.*929C>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 0.165 in 153,308 control chromosomes in the GnomAD database, including 2,658 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 0.17 (2640 hom., cov: 34)
  • Exomes 𝑓: 0.18 (18 hom.)
• Consequence: OSBPL5 NM_020896.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OSBPL5	NM_020896.4	c.*929C>T		3_prime_UTR_variant	22/22	ENST00000263650.12	NP_065947.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OSBPL5	ENST00000263650.12	c.*929C>T		3_prime_UTR_variant	22/22	1	NM_020896.4	ENSP00000263650	P1
OSBPL5	ENST00000389989.7	c.*929C>T		3_prime_UTR_variant	21/21	1		ENSP00000374639
OSBPL5	ENST00000478260.5	c.*929C>T		3_prime_UTR_variant	8/8	2		ENSP00000437141

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25127 AN: 152100 Hom.: 2639 Cov.: 34

Gnomad AFR AF: 0.0565

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.153

GnomAD4 exome AF: 0.183 AC: 199 AN: 1090 Hom.: 18 Cov.: 0 AF XY: 0.186 AC XY: 110 AN XY: 590

Gnomad4 AFR exome AF: 0.0357

Gnomad4 AMR exome AF: 0.125

Gnomad4 ASJ exome AF: 0.00

Gnomad4 SAS exome AF: 0.158

Gnomad4 FIN exome AF: 0.228

Gnomad4 NFE exome AF: 0.181

Gnomad4 OTH exome AF: 0.132

GnomAD4 genome AF: 0.165 AC: 25126 AN: 152218 Hom.: 2640 Cov.: 34 AF XY: 0.163 AC XY: 12147 AN XY: 74418

Gnomad4 AFR AF: 0.0564

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.00463

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.151

Alfa AF: 0.215 Hom.: 2840

Bravo AF: 0.151

Asia WGS AF: 0.0630 AC: 221 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.87

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: rs8813; hg19: chr11-3108506; COSMIC: COSV55147099; COSMIC: COSV55147099;