rs2013777

Positions:

• chr3-31675639-A-C
• chr3-31675639-A-T

Variant summary

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

The NM_017784.5(OSBPL10):​c.1727-4656T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 152,020 control chromosomes in the GnomAD database, including 21,502 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 0.50 (21502 hom., cov: 32)
• Consequence: OSBPL10 NM_017784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL10	NM_017784.5	c.1727-4656T>G		intron_variant		ENST00000396556.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL10	ENST00000396556.7	c.1727-4656T>G		intron_variant		1	NM_017784.5	P2
OSBPL10	ENST00000429492.6	c.1033-4656T>G		intron_variant		2
OSBPL10	ENST00000438237.6	c.1535-4656T>G		intron_variant		2		A2

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75412 AN: 151904 Hom.: 21461 Cov.: 32

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.497 AC: 75506 AN: 152020 Hom.: 21502 Cov.: 32 AF XY: 0.496 AC XY: 36855 AN XY: 74320

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.495

Alfa AF: 0.392 Hom.: 5776

Bravo AF: 0.513

Asia WGS AF: 0.542 AC: 1884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.62

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: rs2013777; hg19: chr3-31717131;