3-31797643-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.729+32397T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 344,112 control chromosomes in the GnomAD database, including 72,039 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 0.58 (27621 hom., cov: 32)
  • Exomes 𝑓: 0.68 (44418 hom.)
• Consequence: OSBPL10 NM_017784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.311

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=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL10	NM_017784.5	c.729+32397T>C		intron_variant		ENST00000396556.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL10	ENST00000396556.7	c.729+32397T>C		intron_variant		1	NM_017784.5	P2

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88602 AN: 152006 Hom.: 27610 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.600

GnomAD4 exome AF: 0.676 AC: 129769 AN: 191988 Hom.: 44418 AF XY: 0.683 AC XY: 72844 AN XY: 106668

Gnomad4 AFR exome AF: 0.350

Gnomad4 AMR exome AF: 0.697

Gnomad4 ASJ exome AF: 0.697

Gnomad4 EAS exome AF: 0.809

Gnomad4 SAS exome AF: 0.714

Gnomad4 FIN exome AF: 0.660

Gnomad4 NFE exome AF: 0.666

Gnomad4 OTH exome AF: 0.660

GnomAD4 genome AF: 0.583 AC: 88625 AN: 152124 Hom.: 27621 Cov.: 32 AF XY: 0.589 AC XY: 43815 AN XY: 74384

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.601

Alfa AF: 0.656 Hom.: 62650

Bravo AF: 0.571

Asia WGS AF: 0.714 AC: 2481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	10
Dann	Benign	0.91

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: rs7653447; hg19: chr3-31839135; COSMIC: COSV67345357; COSMIC: COSV67345357;