rs2290531

Positions:

• chr3-31747792-T-C

Variant summary

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

The NM_017784.5(OSBPL10):​c.940+118A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 1,045,268 control chromosomes in the GnomAD database, including 157,970 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 0.51 (20520 hom., cov: 32)
  • Exomes 𝑓: 0.55 (137450 hom.)
• Consequence: OSBPL10 NM_017784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.968

Genes affected

OSBPL10 (HGNC:16395): (oxysterol binding protein like 10) 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. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]

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 = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL10	NM_017784.5	c.940+118A>G		intron_variant		ENST00000396556.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL10	ENST00000396556.7	c.940+118A>G		intron_variant		1	NM_017784.5	P2

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77888 AN: 151860 Hom.: 20513 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.509

GnomAD4 exome AF: 0.549 AC: 490563 AN: 893290 Hom.: 137450 AF XY: 0.549 AC XY: 251215 AN XY: 457542

Gnomad4 AFR exome AF: 0.412

Gnomad4 AMR exome AF: 0.711

Gnomad4 ASJ exome AF: 0.485

Gnomad4 EAS exome AF: 0.794

Gnomad4 SAS exome AF: 0.578

Gnomad4 FIN exome AF: 0.524

Gnomad4 NFE exome AF: 0.532

Gnomad4 OTH exome AF: 0.528

GnomAD4 genome AF: 0.513 AC: 77928 AN: 151978 Hom.: 20520 Cov.: 32 AF XY: 0.516 AC XY: 38303 AN XY: 74284

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.507

Alfa AF: 0.525 Hom.: 9701

Bravo AF: 0.516

Asia WGS AF: 0.604 AC: 2102 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	0.39
DANN	Benign	0.30

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: rs2290531; hg19: chr3-31789284;