chr3-125594988-G-A

Position:

• chr3-125594988-G-A

Variant summary

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

The NM_022776.5(OSBPL11):​c.-188C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0562 in 597,580 control chromosomes in the GnomAD database, including 1,305 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 0.074 (588 hom., cov: 32)
  • Exomes 𝑓: 0.050 (717 hom.)
• Consequence: OSBPL11 NM_022776.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724

Genes affected

OSBPL11 (HGNC:16397): (oxysterol binding protein like 11) This gene encodes a member of the oxysterol-binding protein (OSBP) family, a group of intracellular lipid receptors. Like most members, the encoded protein contains an N-terminal pleckstrin homology domain and a highly conserved C-terminal OSBP-like sterol-binding domain. [provided by RefSeq, Jul 2008]

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 (AFR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OSBPL11	NM_022776.5	c.-188C>T		5_prime_UTR_variant	1/13	ENST00000296220.6	NP_073613.2
OSBPL11	XM_047447396.1	c.-188C>T		5_prime_UTR_variant	1/9		XP_047303352.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OSBPL11	ENST00000296220.6	c.-188C>T		5_prime_UTR_variant	1/13	1	NM_022776.5	ENSP00000296220	P1

Frequencies

GnomAD3 genomes AF: 0.0744 AC: 11314 AN: 152068 Hom.: 589 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0798

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.0614

Gnomad SAS AF: 0.0593

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0400

Gnomad OTH AF: 0.0651

GnomAD4 exome AF: 0.0499 AC: 22229 AN: 445394 Hom.: 717 Cov.: 6 AF XY: 0.0495 AC XY: 11474 AN XY: 231840

Gnomad4 AFR exome AF: 0.156

Gnomad4 AMR exome AF: 0.0867

Gnomad4 ASJ exome AF: 0.0365

Gnomad4 EAS exome AF: 0.0778

Gnomad4 SAS exome AF: 0.0573

Gnomad4 FIN exome AF: 0.0268

Gnomad4 NFE exome AF: 0.0415

Gnomad4 OTH exome AF: 0.0532

GnomAD4 genome AF: 0.0744 AC: 11330 AN: 152186 Hom.: 588 Cov.: 32 AF XY: 0.0730 AC XY: 5429 AN XY: 74410

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.0797

Gnomad4 ASJ AF: 0.0386

Gnomad4 EAS AF: 0.0620

Gnomad4 SAS AF: 0.0589

Gnomad4 FIN AF: 0.0262

Gnomad4 NFE AF: 0.0400

Gnomad4 OTH AF: 0.0663

Alfa AF: 0.0536 Hom.: 74

Bravo AF: 0.0823

Asia WGS AF: 0.0640 AC: 223 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	2.8
DANN	Benign	0.80

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: rs1055419; hg19: chr3-125313832;