3-31670901-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_017784.5(OSBPL10):c.1809G>A(p.Pro603=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 1,613,690 control chromosomes in the GnomAD database, including 127,974 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 0.49 (20928 hom., cov: 32)
  • Exomes 𝑓: 0.37 (107046 hom.)
• Consequence: OSBPL10 NM_017784.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -6.33

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP7: Synonymous conserved (PhyloP=-6.33 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL10	NM_017784.5	c.1809G>A	p.Pro603=	synonymous_variant	9/12	ENST00000396556.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL10	ENST00000396556.7	c.1809G>A	p.Pro603=	synonymous_variant	9/12	1	NM_017784.5	P2
OSBPL10	ENST00000438237.6	c.1617G>A	p.Pro539=	synonymous_variant	8/11	2		A2
OSBPL10	ENST00000429492.6	c.1116G>A	p.Pro372=	synonymous_variant	6/8	2

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74371 AN: 151886 Hom.: 20878 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.493

GnomAD3 exomes AF: 0.421 AC: 105656 AN: 251254 Hom.: 24403 AF XY: 0.414 AC XY: 56197 AN XY: 135798

Gnomad AFR exome AF: 0.776

Gnomad AMR exome AF: 0.361

Gnomad ASJ exome AF: 0.483

Gnomad EAS exome AF: 0.678

Gnomad SAS exome AF: 0.397

Gnomad FIN exome AF: 0.366

Gnomad NFE exome AF: 0.358

Gnomad OTH exome AF: 0.414

GnomAD4 exome AF: 0.372 AC: 544358 AN: 1461686 Hom.: 107046 Cov.: 44 AF XY: 0.373 AC XY: 270859 AN XY: 727120

Gnomad4 AFR exome AF: 0.784

Gnomad4 AMR exome AF: 0.367

Gnomad4 ASJ exome AF: 0.482

Gnomad4 EAS exome AF: 0.667

Gnomad4 SAS exome AF: 0.400

Gnomad4 FIN exome AF: 0.372

Gnomad4 NFE exome AF: 0.343

Gnomad4 OTH exome AF: 0.410

GnomAD4 genome AF: 0.490 AC: 74476 AN: 152004 Hom.: 20928 Cov.: 32 AF XY: 0.490 AC XY: 36375 AN XY: 74306

Gnomad4 AFR AF: 0.771

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.494

Alfa AF: 0.378 Hom.: 20693

Bravo AF: 0.506

Asia WGS AF: 0.536 AC: 1865 AN: 3478

EpiCase AF: 0.367

EpiControl AF: 0.366

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.030
Dann	Benign	0.62
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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: rs3749405; hg19: chr3-31712393; COSMIC: COSV67339421;