3-31959550-C-A

Variant names:

• chr3-31959550-C-A
• rs9847800
• NM_017784.5:c.281+21349G>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.281+21349G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 152,006 control chromosomes in the GnomAD database, including 30,931 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 0.62 (30931 hom., cov: 32)
• Consequence: OSBPL10 NM_017784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.449
• 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=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL10	NM_017784.5	c.281+21349G>T		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+21349G>T		intron_variant	Intron 1 of 11	1	NM_017784.5	ENSP00000379804.2

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94143 AN: 151888 Hom.: 30878 Cov.: 32

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.620 AC: 94256 AN: 152006 Hom.: 30931 Cov.: 32 AF XY: 0.628 AC XY: 46623 AN XY: 74278

African (AFR) AF: 0.838 AC: 34768 AN: 41502

American (AMR) AF: 0.602 AC: 9187 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1614 AN: 3464

East Asian (EAS) AF: 0.749 AC: 3868 AN: 5166

South Asian (SAS) AF: 0.694 AC: 3336 AN: 4808

European-Finnish (FIN) AF: 0.586 AC: 6187 AN: 10556

Middle Eastern (MID) AF: 0.541 AC: 158 AN: 292

European-Non Finnish (NFE) AF: 0.493 AC: 33464 AN: 67938

Other (OTH) AF: 0.596 AC: 1258 AN: 2110

Alfa AF: 0.529 Hom.: 93510

Bravo AF: 0.632

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	5.5
DANN	Benign	0.62
PhyloP100		0.45
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: rs9847800; hg19: chr3-32001042;