chr11-3088178-C-T

Position:

• chr11-3088178-C-T

Variant summary

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

The NM_020896.4(OSBPL5):​c.*27G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 1,527,110 control chromosomes in the GnomAD database, including 384,217 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 0.72 (39003 hom., cov: 33)
  • Exomes 𝑓: 0.71 (345214 hom.)
• Consequence: OSBPL5 NM_020896.4 3_prime_UTR
• Scores: Splicing: ADA: 0.00006899
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

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]

OSBPL5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OSBPL5	NM_020896.4	c.*27G>A		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	c.*27G>A		3_prime_UTR_variant	22/22	1	NM_020896.4	ENSP00000263650.7

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108550 AN: 151618 Hom.: 38957 Cov.: 33

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.684

GnomAD3 exomes AF: 0.715 AC: 135028 AN: 188864 Hom.: 48560 AF XY: 0.717 AC XY: 72509 AN XY: 101176

Gnomad AFR exome AF: 0.738

Gnomad AMR exome AF: 0.731

Gnomad ASJ exome AF: 0.650

Gnomad EAS exome AF: 0.810

Gnomad SAS exome AF: 0.833

Gnomad FIN exome AF: 0.684

Gnomad NFE exome AF: 0.679

Gnomad OTH exome AF: 0.665

GnomAD4 exome AF: 0.706 AC: 971686 AN: 1375374 Hom.: 345214 Cov.: 31 AF XY: 0.710 AC XY: 480440 AN XY: 676586

Gnomad4 AFR exome AF: 0.744

Gnomad4 AMR exome AF: 0.728

Gnomad4 ASJ exome AF: 0.661

Gnomad4 EAS exome AF: 0.842

Gnomad4 SAS exome AF: 0.833

Gnomad4 FIN exome AF: 0.696

Gnomad4 NFE exome AF: 0.693

Gnomad4 OTH exome AF: 0.700

GnomAD4 genome AF: 0.716 AC: 108652 AN: 151736 Hom.: 39003 Cov.: 33 AF XY: 0.721 AC XY: 53493 AN XY: 74160

Gnomad4 AFR AF: 0.746

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.816

Gnomad4 SAS AF: 0.838

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.687

Alfa AF: 0.643 Hom.: 4000

Bravo AF: 0.714

Asia WGS AF: 0.824 AC: 2866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.7
DANN	Benign	0.67

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000069
dbscSNV1_RF	Benign	0.0060
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: rs2289998; hg19: chr11-3109408; COSMIC: COSV55141855; COSMIC: COSV55141855;