chr3-31757762-T-C

Variant names:

• chr3-31757762-T-C
• rs2045298
• NM_017784.5:c.730-9642A>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.730-9642A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,096 control chromosomes in the GnomAD database, including 28,995 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 0.57 (28995 hom., cov: 33)
• Consequence: OSBPL10 NM_017784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614
• Publications: 4 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 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.730-9642A>G		intron	N/A	NP_060254.2
	OSBPL10	NM_001174060.2		c.538-9642A>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.730-9642A>G		intron	N/A	ENSP00000379804.2	Q9BXB5-1
	OSBPL10	ENST00000959571.1		c.625-9642A>G		intron	N/A	ENSP00000629630.1
	OSBPL10	ENST00000911816.1		c.730-9642A>G		intron	N/A	ENSP00000581875.1

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86681 AN: 151976 Hom.: 28988 Cov.: 33

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.600

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.570 AC: 86694 AN: 152096 Hom.: 28995 Cov.: 33 AF XY: 0.577 AC XY: 42912 AN XY: 74366

African (AFR) AF: 0.191 AC: 7902 AN: 41478

American (AMR) AF: 0.695 AC: 10620 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2522 AN: 3472

East Asian (EAS) AF: 0.843 AC: 4365 AN: 5178

South Asian (SAS) AF: 0.726 AC: 3504 AN: 4828

European-Finnish (FIN) AF: 0.704 AC: 7441 AN: 10574

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48314 AN: 67974

Other (OTH) AF: 0.601 AC: 1271 AN: 2116

Alfa AF: 0.625 Hom.: 13963

Bravo AF: 0.551

Asia WGS AF: 0.724 AC: 2514 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.59
DANN	Benign	0.48
PhyloP100		-0.61
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: rs2045298; hg19: chr3-31799254;