chr3-31947995-A-C

Variant names:

• chr3-31947995-A-C
• rs9853939
• NM_017784.5:c.281+32904T>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.281+32904T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,064 control chromosomes in the GnomAD database, including 26,925 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 0.57 (26925 hom., cov: 32)
• Consequence: OSBPL10 NM_017784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL10	NM_017784.5	c.281+32904T>G		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+32904T>G		intron_variant	Intron 1 of 11	1	NM_017784.5	ENSP00000379804.2

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86324 AN: 151946 Hom.: 26858 Cov.: 32

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.569 AC: 86449 AN: 152064 Hom.: 26925 Cov.: 32 AF XY: 0.571 AC XY: 42465 AN XY: 74328

African (AFR) AF: 0.843 AC: 34985 AN: 41518

American (AMR) AF: 0.516 AC: 7895 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1421 AN: 3470

East Asian (EAS) AF: 0.527 AC: 2713 AN: 5148

South Asian (SAS) AF: 0.567 AC: 2736 AN: 4824

European-Finnish (FIN) AF: 0.482 AC: 5089 AN: 10550

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29940 AN: 67954

Other (OTH) AF: 0.548 AC: 1157 AN: 2112

Alfa AF: 0.503 Hom.: 39794

Bravo AF: 0.582

Asia WGS AF: 0.555 AC: 1928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.42
PhyloP100		-0.039
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: rs9853939; hg19: chr3-31989487;