rs1053746

Variant names:

• chr11-3087455-G-A
• rs1053746
• NM_020896.4:c.*750C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-3087455-G-A
• chr11-3087455-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
OSBPL5	NM_020896.4	c.*750C>T		3_prime_UTR_variant	Exon 22 of 22	ENST00000263650.12	NP_065947.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSBPL5	ENST00000263650.12	c.*750C>T		3_prime_UTR_variant	Exon 22 of 22	1	NM_020896.4	ENSP00000263650.7

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

African (AFR) AF: 0.0286 AC: 2 AN: 70

American (AMR) AF: 0.00 AC: 0 AN: 8

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AF: 0.0938 AC: 9 AN: 96

European-Finnish (FIN) AF: 0.0556 AC: 5 AN: 90

Middle Eastern (MID) AF: 0.0236 AC: 35 AN: 1484

European-Non Finnish (NFE) AF: 0.0120 AC: 3 AN: 250

Other (OTH) AF: 0.0536 AC: 9 AN: 168

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

African (AFR) AF: 0.0695 AC: 2887 AN: 41516

American (AMR) AF: 0.0179 AC: 274 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0531 AC: 184 AN: 3468

East Asian (EAS) AF: 0.00291 AC: 15 AN: 5162

South Asian (SAS) AF: 0.0706 AC: 341 AN: 4830

European-Finnish (FIN) AF: 0.0382 AC: 405 AN: 10606

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0299 AC: 2032 AN: 68010

Other (OTH) AF: 0.0318 AC: 67 AN: 2108

Alfa AF: 0.0326 Hom.: 249

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
PhyloP100		-0.54
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1053746; hg19: chr11-3108685;