rs7643025

Variant names:

• chr3-31797750-T-C
• rs7643025
• NM_017784.5:c.729+32290A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-31797750-T-C
• chr3-31797750-T-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.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
• Publications: 11 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 (AFR) allele frequency at 95% confidence interval = 0.855 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL10	NM_017784.5	MANE Select	c.729+32290A>G		intron	N/A	NP_060254.2
	OSBPL10	NM_001174060.2		c.538-49630A>G		intron	N/A	NP_001167531.1	Q9BXB5-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL10	ENST00000396556.7	TSL:1 MANE Select	c.729+32290A>G		intron	N/A	ENSP00000379804.2	Q9BXB5-1
	OSBPL10	ENST00000959571.1		c.624+5A>G		splice_region intron	N/A	ENSP00000629630.1
	OSBPL10	ENST00000911816.1		c.729+32290A>G		intron	N/A	ENSP00000581875.1

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

GnomAD2 exomes AF: 0.764 AC: 104141 AN: 136272 AF XY: 0.765

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 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

African (AFR) AF: 0.868 AC: 7406 AN: 8532

American (AMR) AF: 0.755 AC: 20458 AN: 27108

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 8210 AN: 10738

East Asian (EAS) AF: 0.822 AC: 7496 AN: 9124

South Asian (SAS) AF: 0.777 AC: 46143 AN: 59378

European-Finnish (FIN) AF: 0.745 AC: 9508 AN: 12762

Middle Eastern (MID) AF: 0.756 AC: 2098 AN: 2776

European-Non Finnish (NFE) AF: 0.740 AC: 116511 AN: 157452

Other (OTH) AF: 0.752 AC: 10632 AN: 14134

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

African (AFR) AF: 0.863 AC: 35827 AN: 41526

American (AMR) AF: 0.765 AC: 11696 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2642 AN: 3472

East Asian (EAS) AF: 0.806 AC: 4157 AN: 5160

South Asian (SAS) AF: 0.773 AC: 3716 AN: 4806

European-Finnish (FIN) AF: 0.761 AC: 8042 AN: 10572

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.738 AC: 50177 AN: 67992

Other (OTH) AF: 0.757 AC: 1601 AN: 2116

Alfa AF: 0.754 Hom.: 139790

Bravo AF: 0.784

Asia WGS AF: 0.799 AC: 2781 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	21
DANN	Benign	0.59
PhyloP100		-0.71
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7643025; hg19: chr3-31839242;