3-31665408-G-A

Variant names:

• chr3-31665408-G-A
• rs3792551
• NM_017784.5:c.2097-1176C>T

Variant summary

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

The NM_017784.5(OSBPL10):​c.2097-1176C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,166 control chromosomes in the GnomAD database, including 1,115 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 0.10 (1115 hom., cov: 32)
• Consequence: OSBPL10 NM_017784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.525
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.25 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL10	NM_017784.5	MANE Select	c.2097-1176C>T		intron	N/A	NP_060254.2
	OSBPL10	NM_001174060.2		c.1905-1176C>T		intron	N/A	NP_001167531.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL10	ENST00000396556.7	TSL:1 MANE Select	c.2097-1176C>T		intron	N/A	ENSP00000379804.2
	OSBPL10	ENST00000438237.6	TSL:2	c.1905-1176C>T		intron	N/A	ENSP00000406124.2
	OSBPL10	ENST00000429492.6	TSL:2	c.1401-1176C>T		intron	N/A	ENSP00000416078.2

Frequencies

GnomAD3 genomes AF: 0.0998 AC: 15167 AN: 152048 Hom.: 1104 Cov.: 32

Gnomad AFR AF: 0.0697

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.0838

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0732

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.100 AC: 15216 AN: 152166 Hom.: 1115 Cov.: 32 AF XY: 0.107 AC XY: 7928 AN XY: 74398

African (AFR) AF: 0.0697 AC: 2897 AN: 41538

American (AMR) AF: 0.257 AC: 3928 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0838 AC: 291 AN: 3472

East Asian (EAS) AF: 0.159 AC: 819 AN: 5146

South Asian (SAS) AF: 0.180 AC: 870 AN: 4822

European-Finnish (FIN) AF: 0.105 AC: 1116 AN: 10588

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0732 AC: 4980 AN: 68002

Other (OTH) AF: 0.117 AC: 246 AN: 2106

Alfa AF: 0.0912 Hom.: 1610

Bravo AF: 0.110

Asia WGS AF: 0.209 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.74
PhyloP100		0.53
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: rs3792551; hg19: chr3-31706900;