chr3-31675639-A-C

Variant names:

• chr3-31675639-A-C
• rs2013777
• NM_017784.5:c.1727-4656T>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.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
• Publications: 2 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL10	NM_017784.5	MANE Select	c.1727-4656T>G		intron	N/A	NP_060254.2
	OSBPL10	NM_001174060.2		c.1535-4656T>G		intron	N/A	NP_001167531.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL10	ENST00000396556.7	TSL:1 MANE Select	c.1727-4656T>G		intron	N/A	ENSP00000379804.2
	OSBPL10	ENST00000438237.6	TSL:2	c.1535-4656T>G		intron	N/A	ENSP00000406124.2
	OSBPL10	ENST00000429492.6	TSL:2	c.1031-4656T>G		intron	N/A	ENSP00000416078.2

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

African (AFR) AF: 0.781 AC: 32398 AN: 41486

American (AMR) AF: 0.407 AC: 6223 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1722 AN: 3468

East Asian (EAS) AF: 0.673 AC: 3469 AN: 5152

South Asian (SAS) AF: 0.412 AC: 1986 AN: 4822

European-Finnish (FIN) AF: 0.383 AC: 4051 AN: 10576

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24269 AN: 67932

Other (OTH) AF: 0.495 AC: 1044 AN: 2108

Alfa AF: 0.395 Hom.: 6609

Bravo AF: 0.513

Asia WGS AF: 0.542 AC: 1884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.62
PhyloP100		-2.6
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: rs2013777; hg19: chr3-31717131;