3-31692180-A-G

Variant names:

• chr3-31692180-A-G
• rs1869849
• NM_017784.5:c.1246-8066T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017784.5(OSBPL10):​c.1246-8066T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,128 control chromosomes in the GnomAD database, including 4,658 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 0.21 (4658 hom., cov: 32)
• Consequence: OSBPL10 NM_017784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 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.1246-8066T>C		intron	N/A	NP_060254.2
	OSBPL10	NM_001174060.2		c.1054-8066T>C		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.1246-8066T>C		intron	N/A	ENSP00000379804.2	Q9BXB5-1
	OSBPL10	ENST00000959571.1		c.1141-8066T>C		intron	N/A	ENSP00000629630.1
	OSBPL10	ENST00000911816.1		c.1096-8066T>C		intron	N/A	ENSP00000581875.1

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32012 AN: 152010 Hom.: 4657 Cov.: 32

Gnomad AFR AF: 0.0739

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.210 AC: 32021 AN: 152128 Hom.: 4658 Cov.: 32 AF XY: 0.219 AC XY: 16287 AN XY: 74360

African (AFR) AF: 0.0737 AC: 3060 AN: 41546

American (AMR) AF: 0.389 AC: 5941 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3468

East Asian (EAS) AF: 0.619 AC: 3192 AN: 5158

South Asian (SAS) AF: 0.277 AC: 1332 AN: 4806

European-Finnish (FIN) AF: 0.232 AC: 2447 AN: 10570

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14289 AN: 67990

Other (OTH) AF: 0.221 AC: 468 AN: 2114

Alfa AF: 0.214 Hom.: 2864

Bravo AF: 0.221

Asia WGS AF: 0.384 AC: 1334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.24
PhyloP100		-1.1
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: rs1869849; hg19: chr3-31733672;