Variant rs935431 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.967

Variant links:

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]

OSBPL5 links:

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ACMG classification

Classification made for transcript

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	Protein	UniProt
OSBPL5	NM_020896.4 link	c.*138C>T		3_prime_UTR_variant	22/22	ENST00000263650.12	NP_065947.1	Q9H0X9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OSBPL5	ENST00000263650 link	c.*138C>T		3_prime_UTR_variant	22/22	1	NM_020896.4	ENSP00000263650.7		Q9H0X9-1

Frequencies

GnomAD3 genomes

AF:

0.0960

AC:

14598

AN:

152108

Hom.:

809

Cov.:

show subpopulations

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.:

AF XY:

0.108

AC XY:

35220

AN XY:

326490

show subpopulations

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.:

AF XY:

0.0917

AC XY:

6822

AN XY:

74402

show subpopulations

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.:

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over