chr3-31940275-T-C

Variant names:

• chr3-31940275-T-C
• rs12630931
• NM_017784.5:c.281+40624A>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.281+40624A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,222 control chromosomes in the GnomAD database, including 3,922 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 (3922 hom., cov: 32)
• Consequence: OSBPL10 NM_017784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.620
• Publications: 7 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 (NFE) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL10	NM_017784.5	c.281+40624A>G		intron_variant	Intron 1 of 11	ENST00000396556.7	NP_060254.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSBPL10	ENST00000396556.7	c.281+40624A>G		intron_variant	Intron 1 of 11	1	NM_017784.5	ENSP00000379804.2

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32091 AN: 152104 Hom.: 3920 Cov.: 32

Gnomad AFR AF: 0.0889

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.211 AC: 32095 AN: 152222 Hom.: 3922 Cov.: 32 AF XY: 0.211 AC XY: 15706 AN XY: 74412

African (AFR) AF: 0.0890 AC: 3698 AN: 41568

American (AMR) AF: 0.174 AC: 2666 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3470

East Asian (EAS) AF: 0.150 AC: 778 AN: 5176

South Asian (SAS) AF: 0.208 AC: 1005 AN: 4826

European-Finnish (FIN) AF: 0.301 AC: 3187 AN: 10572

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19118 AN: 68010

Other (OTH) AF: 0.211 AC: 444 AN: 2108

Alfa AF: 0.252 Hom.: 3596

Bravo AF: 0.196

Asia WGS AF: 0.173 AC: 602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.51
PhyloP100		0.62
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: rs12630931; hg19: chr3-31981767;