rs935431

chr11-3088067-G-Achr11-3088067-G-C

Variant summary

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

The NM_020896.4(OSBPL5):c.*138C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 804,802 control chromosomes in the GnomAD database, including 5,417 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 0.096 (808 hom., cov: 34)
  • Exomes 𝑓: 0.11 (4609 hom.)
• Consequence: OSBPL5 NM_020896.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.967

Genes affected

OSBPL5 (HGNC:16392): (oxysterol binding protein like 5) This gene encodes a member of the oxysterol-binding protein (OSBP) family, a group of intracellular lipid receptors that play a key role in the maintenance of cholesterol balance in the body. Most members contain an N-terminal pleckstrin homology domain and a highly conserved C-terminal OSBP-like sterol-binding domain. This gene has been shown to be imprinted, with preferential expression from the maternal allele only in placenta. Transcript variants encoding different isoforms have been identified. [provided by RefSeq, Oct 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL5	NM_020896.4	c.*138C>T		3_prime_UTR_variant	22/22	ENST00000263650.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL5	ENST00000263650.12	c.*138C>T		3_prime_UTR_variant	22/22	1	NM_020896.4	P1

Frequencies

GnomAD3 genomes AF: 0.0960 AC: 14598 AN: 152108 Hom.: 809 Cov.: 34

Gnomad AFR AF: 0.0573

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.0458

Gnomad FIN AF: 0.0633

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.130

GnomAD4 exome AF: 0.110 AC: 71576 AN: 652576 Hom.: 4609 Cov.: 9 AF XY: 0.108 AC XY: 35220 AN XY: 326490

Gnomad4 AFR exome AF: 0.0602

Gnomad4 AMR exome AF: 0.159

Gnomad4 ASJ exome AF: 0.139

Gnomad4 EAS exome AF: 0.00505

Gnomad4 SAS exome AF: 0.0510

Gnomad4 FIN exome AF: 0.0664

Gnomad4 NFE exome AF: 0.121

Gnomad4 OTH exome AF: 0.112

GnomAD4 genome AF: 0.0959 AC: 14594 AN: 152226 Hom.: 808 Cov.: 34 AF XY: 0.0917 AC XY: 6822 AN XY: 74402

Gnomad4 AFR AF: 0.0571

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.0139

Gnomad4 SAS AF: 0.0460

Gnomad4 FIN AF: 0.0633

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.128

Alfa AF: 0.0453 Hom.: 34

Bravo AF: 0.104

Asia WGS AF: 0.0320 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.048
Dann	Benign	0.75

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: rs935431; hg19: chr11-3109297; COSMIC: COSV55143149; COSMIC: COSV55143149;