rs12171283

chr3-31780845-C-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_017784.5(OSBPL10):c.730-32725G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.37 (1188 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: OSBPL10 NM_017784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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 Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL10	NM_017784.5	c.730-32725G>T		intron_variant		ENST00000396556.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL10	ENST00000396556.7	c.730-32725G>T		intron_variant		1	NM_017784.5	P2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 12987 AN: 34728 Hom.: 1172 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.371

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.303

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.375 AC: 13044 AN: 34822 Hom.: 1188 Cov.: 0 AF XY: 0.376 AC XY: 6321 AN XY: 16804

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.298

Alfa AF: 0.708 Hom.: 13049

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.91
Dann	Benign	0.24

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: rs12171283; hg19: chr3-31822337;