rs11058

chr3-31661972-T-C

Variant summary

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

The NM_017784.5(OSBPL10):c.*100A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 1,496,114 control chromosomes in the GnomAD database, including 29,840 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 0.20 (3145 hom., cov: 32)
  • Exomes 𝑓: 0.20 (26695 hom.)
• Consequence: OSBPL10 NM_017784.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL10	NM_017784.5	c.*100A>G		3_prime_UTR_variant	12/12	ENST00000396556.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL10	ENST00000396556.7	c.*100A>G		3_prime_UTR_variant	12/12	1	NM_017784.5	P2
OSBPL10	ENST00000429492.6	c.*2047A>G		3_prime_UTR_variant	8/8	2
OSBPL10	ENST00000438237.6	c.*100A>G		3_prime_UTR_variant	11/11	2		A2

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30684 AN: 151882 Hom.: 3141 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.208

GnomAD4 exome AF: 0.197 AC: 265240 AN: 1344112 Hom.: 26695 Cov.: 19 AF XY: 0.196 AC XY: 130888 AN XY: 666444

Gnomad4 AFR exome AF: 0.189

Gnomad4 AMR exome AF: 0.270

Gnomad4 ASJ exome AF: 0.247

Gnomad4 EAS exome AF: 0.309

Gnomad4 SAS exome AF: 0.184

Gnomad4 FIN exome AF: 0.196

Gnomad4 NFE exome AF: 0.190

Gnomad4 OTH exome AF: 0.200

GnomAD4 genome AF: 0.202 AC: 30707 AN: 152002 Hom.: 3145 Cov.: 32 AF XY: 0.201 AC XY: 14953 AN XY: 74286

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.205

Alfa AF: 0.201 Hom.: 1682

Bravo AF: 0.208

Asia WGS AF: 0.209 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	12
Dann	Benign	0.71

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: rs11058; hg19: chr3-31703464; COSMIC: COSV67345355; COSMIC: COSV67345355;