rs6803685

chr3-31708233-C-T

Variant summary

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

The NM_017784.5(OSBPL10):c.1096-5725G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 152,072 control chromosomes in the GnomAD database, including 31,784 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 0.64 (31784 hom., cov: 32)
• Consequence: OSBPL10 NM_017784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

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]

OSBPL10-AS1 (HGNC:40767): (OSBPL10 antisense RNA 1)

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 (NFE) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL10	NM_017784.5	c.1096-5725G>A		intron_variant		ENST00000396556.7
OSBPL10-AS1	NR_049771.1	n.28-2705C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL10	ENST00000396556.7	c.1096-5725G>A		intron_variant		1	NM_017784.5	P2
OSBPL10-AS1	ENST00000428872.6	n.28-2705C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96933 AN: 151952 Hom.: 31763 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.638 AC: 96989 AN: 152072 Hom.: 31784 Cov.: 32 AF XY: 0.631 AC XY: 46866 AN XY: 74318

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.645

Alfa AF: 0.687 Hom.: 4553

Bravo AF: 0.615

Asia WGS AF: 0.530 AC: 1846 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	0.64
Dann	Benign	0.39

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: rs6803685; hg19: chr3-31749725;