rs12632849

Variant names:

• chr3-31751426-G-A
• rs12632849
• NM_017784.5:c.730-3306C>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.730-3306C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,024 control chromosomes in the GnomAD database, including 8,357 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 0.30 (8357 hom., cov: 32)
• Consequence: OSBPL10 NM_017784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL10	NM_017784.5	c.730-3306C>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.730-3306C>T		intron_variant	Intron 4 of 11	1	NM_017784.5	ENSP00000379804.2

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45344 AN: 151906 Hom.: 8358 Cov.: 32

Gnomad AFR AF: 0.0919

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.298 AC: 45347 AN: 152024 Hom.: 8357 Cov.: 32 AF XY: 0.304 AC XY: 22604 AN XY: 74296

African (AFR) AF: 0.0917 AC: 3804 AN: 41478

American (AMR) AF: 0.434 AC: 6628 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1176 AN: 3470

East Asian (EAS) AF: 0.629 AC: 3247 AN: 5162

South Asian (SAS) AF: 0.389 AC: 1868 AN: 4806

European-Finnish (FIN) AF: 0.350 AC: 3687 AN: 10540

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23894 AN: 67976

Other (OTH) AF: 0.309 AC: 653 AN: 2110

Alfa AF: 0.325 Hom.: 16633

Bravo AF: 0.295

Asia WGS AF: 0.417 AC: 1451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.7
DANN	Benign	0.80
PhyloP100		0.20
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: rs12632849; hg19: chr3-31792918;