chr1-51729357-C-T

Position:

• chr1-51729357-C-T

Variant summary

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

The NM_024586.6(OSBPL9):​c.318+15278C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0878 in 152,306 control chromosomes in the GnomAD database, including 878 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 0.088 (878 hom., cov: 32)
  • Exomes 𝑓: 0.061 (0 hom.)
• Consequence: OSBPL9 NM_024586.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.941

Genes affected

OSBPL9 (HGNC:16386): (oxysterol binding protein like 9) 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 some members contain only the sterol-binding domain. This family member functions as a cholesterol transfer protein that regulates Golgi structure and function. Multiple transcript variants, most of which encode distinct isoforms, have been identified. Related pseudogenes have been identified on chromosomes 3, 11 and 12. [provided by RefSeq, Jul 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OSBPL9	NM_024586.6	c.318+15278C>T		intron_variant		ENST00000428468.6	NP_078862.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OSBPL9	ENST00000428468.6	c.318+15278C>T		intron_variant		1	NM_024586.6	ENSP00000407168	P4

Frequencies

GnomAD3 genomes AF: 0.0877 AC: 13335 AN: 152094 Hom.: 867 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.0580

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.0391

Gnomad FIN AF: 0.0338

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0530

Gnomad OTH AF: 0.0803

GnomAD4 exome AF: 0.0612 AC: 6 AN: 98 Hom.: 0 Cov.: 0 AF XY: 0.0500 AC XY: 4 AN XY: 80

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.0349

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.0878 AC: 13359 AN: 152208 Hom.: 878 Cov.: 32 AF XY: 0.0869 AC XY: 6469 AN XY: 74416

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.0579

Gnomad4 ASJ AF: 0.0216

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.0392

Gnomad4 FIN AF: 0.0338

Gnomad4 NFE AF: 0.0530

Gnomad4 OTH AF: 0.0908

Alfa AF: 0.0600 Hom.: 329

Bravo AF: 0.0948

Asia WGS AF: 0.177 AC: 613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.94
DANN	Benign	0.81

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: rs856600; hg19: chr1-52195029;