rs7643025

Positions:

• chr3-31797750-T-C
• chr3-31797750-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017784.5(OSBPL10):​c.729+32290A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 454,144 control chromosomes in the GnomAD database, including 133,239 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 0.78 (46549 hom., cov: 32)
  • Exomes 𝑓: 0.76 (86690 hom.)
• Consequence: OSBPL10 NM_017784.5 intron
• Scores: Splicing: ADA: 0.00005103
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.712

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]

OSBPL10 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OSBPL10	NM_017784.5	c.729+32290A>G		intron_variant		ENST00000396556.7	NP_060254.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OSBPL10	ENST00000396556.7	c.729+32290A>G		intron_variant		1	NM_017784.5	ENSP00000379804.2

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118594 AN: 152022 Hom.: 46498 Cov.: 32

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.757

GnomAD3 exomes AF: 0.764 AC: 104141 AN: 136272 Hom.: 39929 AF XY: 0.765 AC XY: 56607 AN XY: 73974

Gnomad AFR exome AF: 0.865

Gnomad AMR exome AF: 0.754

Gnomad ASJ exome AF: 0.767

Gnomad EAS exome AF: 0.830

Gnomad SAS exome AF: 0.778

Gnomad FIN exome AF: 0.754

Gnomad NFE exome AF: 0.741

Gnomad OTH exome AF: 0.737

GnomAD4 exome AF: 0.756 AC: 228462 AN: 302004 Hom.: 86690 Cov.: 0 AF XY: 0.759 AC XY: 130441 AN XY: 171928

Gnomad4 AFR exome AF: 0.868

Gnomad4 AMR exome AF: 0.755

Gnomad4 ASJ exome AF: 0.765

Gnomad4 EAS exome AF: 0.822

Gnomad4 SAS exome AF: 0.777

Gnomad4 FIN exome AF: 0.745

Gnomad4 NFE exome AF: 0.740

Gnomad4 OTH exome AF: 0.752

GnomAD4 genome AF: 0.780 AC: 118701 AN: 152140 Hom.: 46549 Cov.: 32 AF XY: 0.782 AC XY: 58106 AN XY: 74350

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.761

Gnomad4 EAS AF: 0.806

Gnomad4 SAS AF: 0.773

Gnomad4 FIN AF: 0.761

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.757

Alfa AF: 0.747 Hom.: 90267

Bravo AF: 0.784

Asia WGS AF: 0.799 AC: 2781 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	21
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000051
dbscSNV1_RF	Benign	0.0
SpliceAI score (max)		0.83		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.83		Position offset: 5

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7643025; hg19: chr3-31839242;