rs7565742

Variant summary

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

The NM_032523.4(OSBPL6):​c.1534-2587C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0829 in 152,198 control chromosomes in the GnomAD database, including 616 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 0.083 ( 616 hom., cov: 31)

Consequence

OSBPL6
NM_032523.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0620
Variant links:
Genes affected
OSBPL6 (HGNC:16388): (oxysterol binding protein like 6) This gene encodes a member of the oxysterol-binding protein (OSBP) family, a group of intracellular lipid receptors. Most members contain an N-terminal pleckstrin homology domain and a highly conserved C-terminal OSBP-like sterol-binding domain. Transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OSBPL6NM_032523.4 linkuse as main transcriptc.1534-2587C>A intron_variant ENST00000190611.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OSBPL6ENST00000190611.9 linkuse as main transcriptc.1534-2587C>A intron_variant 1 NM_032523.4 A1Q9BZF3-1

Frequencies

GnomAD3 genomes
AF:
0.0827
AC:
12584
AN:
152080
Hom.:
610
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.114
Gnomad AMI
AF:
0.0493
Gnomad AMR
AF:
0.0530
Gnomad ASJ
AF:
0.0605
Gnomad EAS
AF:
0.00462
Gnomad SAS
AF:
0.0551
Gnomad FIN
AF:
0.0948
Gnomad MID
AF:
0.0665
Gnomad NFE
AF:
0.0781
Gnomad OTH
AF:
0.0875
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0829
AC:
12622
AN:
152198
Hom.:
616
Cov.:
31
AF XY:
0.0827
AC XY:
6154
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.114
Gnomad4 AMR
AF:
0.0530
Gnomad4 ASJ
AF:
0.0605
Gnomad4 EAS
AF:
0.00463
Gnomad4 SAS
AF:
0.0553
Gnomad4 FIN
AF:
0.0948
Gnomad4 NFE
AF:
0.0781
Gnomad4 OTH
AF:
0.0861
Alfa
AF:
0.0792
Hom.:
639
Bravo
AF:
0.0823
Asia WGS
AF:
0.0370
AC:
128
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
9.9
DANN
Benign
0.53

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.

Other links and lift over

dbSNP: rs7565742; hg19: chr2-179244560; API