rs2290531

Variant names:

• chr3-31747792-T-C
• rs2290531
• NM_017784.5:c.940+118A>G

Variant summary

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

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017784.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL10	NM_017784.5	MANE Select	c.940+118A>G		intron	N/A	NP_060254.2
	OSBPL10	NM_001174060.2		c.748+118A>G		intron	N/A	NP_001167531.1	Q9BXB5-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL10	ENST00000396556.7	TSL:1 MANE Select	c.940+118A>G		intron	N/A	ENSP00000379804.2	Q9BXB5-1
	OSBPL10	ENST00000959571.1		c.835+118A>G		intron	N/A	ENSP00000629630.1
	OSBPL10	ENST00000911816.1		c.940+118A>G		intron	N/A	ENSP00000581875.1

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

African (AFR) AF: 0.412 AC: 9199 AN: 22338

American (AMR) AF: 0.711 AC: 28438 AN: 39996

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 9702 AN: 20016

East Asian (EAS) AF: 0.794 AC: 29029 AN: 36578

South Asian (SAS) AF: 0.578 AC: 39334 AN: 68064

European-Finnish (FIN) AF: 0.524 AC: 23046 AN: 43986

Middle Eastern (MID) AF: 0.457 AC: 1346 AN: 2948

European-Non Finnish (NFE) AF: 0.532 AC: 328705 AN: 618132

Other (OTH) AF: 0.528 AC: 21764 AN: 41232

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

African (AFR) AF: 0.409 AC: 16934 AN: 41446

American (AMR) AF: 0.628 AC: 9591 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1703 AN: 3470

East Asian (EAS) AF: 0.778 AC: 4015 AN: 5158

South Asian (SAS) AF: 0.576 AC: 2775 AN: 4818

European-Finnish (FIN) AF: 0.503 AC: 5305 AN: 10550

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.529 AC: 35953 AN: 67954

Other (OTH) AF: 0.507 AC: 1067 AN: 2106

Alfa AF: 0.512 Hom.: 15545

Bravo AF: 0.516

Asia WGS AF: 0.604 AC: 2102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.39
DANN	Benign	0.30
PhyloP100		-0.97
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2290531;

hg19: chr3-31789284;