3-31779192-G-A

Variant names:

• chr3-31779192-G-A
• rs11709187
• NM_017784.5:c.730-31072C>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.730-31072C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 152,004 control chromosomes in the GnomAD database, including 24,225 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 0.54 (24225 hom., cov: 32)
• Consequence: OSBPL10 NM_017784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL10	NM_017784.5	c.730-31072C>T		intron_variant	Intron 4 of 11	ENST00000396556.7	NP_060254.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSBPL10	ENST00000396556.7	c.730-31072C>T		intron_variant	Intron 4 of 11	1	NM_017784.5	ENSP00000379804.2

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81374 AN: 151886 Hom.: 24221 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.535 AC: 81384 AN: 152004 Hom.: 24225 Cov.: 32 AF XY: 0.541 AC XY: 40218 AN XY: 74286

African (AFR) AF: 0.250 AC: 10368 AN: 41450

American (AMR) AF: 0.632 AC: 9650 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2268 AN: 3468

East Asian (EAS) AF: 0.791 AC: 4082 AN: 5162

South Asian (SAS) AF: 0.677 AC: 3263 AN: 4820

European-Finnish (FIN) AF: 0.665 AC: 7020 AN: 10552

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.631 AC: 42880 AN: 67964

Other (OTH) AF: 0.558 AC: 1179 AN: 2112

Alfa AF: 0.568 Hom.: 3424

Bravo AF: 0.519

Asia WGS AF: 0.689 AC: 2397 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.66
PhyloP100		-1.8
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: rs11709187; hg19: chr3-31820684;