3-31832522-A-G

Position:

• chr3-31832522-A-G

Variant summary

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

The NM_017784.5(OSBPL10):​c.538-2291T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 151,968 control chromosomes in the GnomAD database, including 21,370 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 0.52 (21370 hom., cov: 32)
• Consequence: OSBPL10 NM_017784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OSBPL10	NM_017784.5	c.538-2291T>C		intron_variant		ENST00000396556.7	NP_060254.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OSBPL10	ENST00000396556.7	c.538-2291T>C		intron_variant		1	NM_017784.5	ENSP00000379804.2

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79170 AN: 151850 Hom.: 21350 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.521 AC: 79240 AN: 151968 Hom.: 21370 Cov.: 32 AF XY: 0.527 AC XY: 39162 AN XY: 74286

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.556

Alfa AF: 0.550 Hom.: 38276

Bravo AF: 0.522

Asia WGS AF: 0.706 AC: 2452 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	0.82
DANN	Benign	0.47

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

Publications

LitVar

Other links and lift over

dbSNP: rs6807471; hg19: chr3-31874014;