ENST00000615516.1:n.1049C>T

Variant names:

• chr20-62232970-C-T
• rs6089695
• ENST00000615516.1:n.1049C>T

Variant summary

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

The ENST00000615516.1(OSBPL2):​n.1049C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 456,016 control chromosomes in the GnomAD database, including 42,938 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 0.37 (12045 hom., cov: 32)
  • Exomes 𝑓: 0.45 (30893 hom.)
• Consequence: OSBPL2 ENST00000615516.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.50

Genes affected

OSBPL2 (HGNC:15761): (oxysterol binding protein like 2) This gene encodes a member of the oxysterol-binding protein (OSBP) family, a group of intracellular lipid receptors. Most members contain an N-terminal pleckstrin homology domain and a highly conserved C-terminal OSBP-like sterol-binding domain, although the encoded protein contains only the sterol-binding domain. In vitro studies have shown that the encoded protein can bind strongly to phosphatic acid and weakly to phosphatidylinositol 3-phosphate, but cannot bind to 25-hydroxycholesterol. The protein associates with the Golgi apparatus. Transcript variants encoding different isoforms have been described. [provided by RefSeq, Sep 2014]

LOC105369209 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369209	NR_160555.1	n.625C>T		non_coding_transcript_exon_variant	Exon 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSBPL2	ENST00000615516.1	n.1049C>T		non_coding_transcript_exon_variant	Exon 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56926 AN: 151888 Hom.: 12050 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.399

GnomAD3 exomes AF: 0.451 AC: 61090 AN: 135510 Hom.: 14217 AF XY: 0.450 AC XY: 33158 AN XY: 73722

Gnomad AFR exome AF: 0.140

Gnomad AMR exome AF: 0.510

Gnomad ASJ exome AF: 0.446

Gnomad EAS exome AF: 0.506

Gnomad SAS exome AF: 0.444

Gnomad FIN exome AF: 0.431

Gnomad NFE exome AF: 0.456

Gnomad OTH exome AF: 0.453

GnomAD4 exome AF: 0.446 AC: 135557 AN: 304010 Hom.: 30893 Cov.: 0 AF XY: 0.447 AC XY: 77426 AN XY: 173102

Gnomad4 AFR exome AF: 0.149

Gnomad4 AMR exome AF: 0.510

Gnomad4 ASJ exome AF: 0.445

Gnomad4 EAS exome AF: 0.512

Gnomad4 SAS exome AF: 0.441

Gnomad4 FIN exome AF: 0.422

Gnomad4 NFE exome AF: 0.452

Gnomad4 OTH exome AF: 0.440

GnomAD4 genome AF: 0.375 AC: 56937 AN: 152006 Hom.: 12045 Cov.: 32 AF XY: 0.378 AC XY: 28049 AN XY: 74278

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.403

Alfa AF: 0.452 Hom.: 21827

Bravo AF: 0.369

Asia WGS AF: 0.512 AC: 1782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.77

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6089695; hg19: chr20-60808026; COSMIC: COSV50778465;