3-31661972-T-C

Variant names:

• chr3-31661972-T-C
• rs11058
• NM_017784.5:c.*100A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017784.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL10	NM_017784.5	MANE Select	c.*100A>G		3_prime_UTR	Exon 12 of 12	NP_060254.2
	OSBPL10	NM_001174060.2		c.*100A>G		3_prime_UTR	Exon 11 of 11	NP_001167531.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL10	ENST00000396556.7	TSL:1 MANE Select	c.*100A>G		3_prime_UTR	Exon 12 of 12	ENSP00000379804.2
	OSBPL10	ENST00000438237.6	TSL:2	c.*100A>G		3_prime_UTR	Exon 11 of 11	ENSP00000406124.2
	OSBPL10	ENST00000429492.6	TSL:2	c.*2047A>G		3_prime_UTR	Exon 8 of 8	ENSP00000416078.2

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

African (AFR) AF: 0.189 AC: 5658 AN: 29982

American (AMR) AF: 0.270 AC: 9338 AN: 34646

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 5480 AN: 22182

East Asian (EAS) AF: 0.309 AC: 11847 AN: 38350

South Asian (SAS) AF: 0.184 AC: 13860 AN: 75426

European-Finnish (FIN) AF: 0.196 AC: 9902 AN: 50490

Middle Eastern (MID) AF: 0.275 AC: 1471 AN: 5356

European-Non Finnish (NFE) AF: 0.190 AC: 196559 AN: 1031926

Other (OTH) AF: 0.200 AC: 11125 AN: 55754

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

African (AFR) AF: 0.184 AC: 7615 AN: 41468

American (AMR) AF: 0.246 AC: 3758 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 837 AN: 3466

East Asian (EAS) AF: 0.276 AC: 1419 AN: 5146

South Asian (SAS) AF: 0.179 AC: 862 AN: 4810

European-Finnish (FIN) AF: 0.197 AC: 2081 AN: 10570

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13430 AN: 67964

Other (OTH) AF: 0.205 AC: 432 AN: 2104

Alfa AF: 0.201 Hom.: 1866

Bravo AF: 0.208

Asia WGS AF: 0.209 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.71
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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