chr2-178379833-C-A

Variant names:

• chr2-178379833-C-A
• rs7565742
• NM_032523.4:c.1534-2587C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
OSBPL6	NM_032523.4	c.1534-2587C>A		intron_variant	Intron 15 of 24	ENST00000190611.9	NP_115912.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSBPL6	ENST00000190611.9	c.1534-2587C>A		intron_variant	Intron 15 of 24	1	NM_032523.4	ENSP00000190611.4

Frequencies

GnomAD3 genomes AF: 0.0827 AC: 12584 AN: 152080 Hom.: 610 Cov.: 31

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

African (AFR) AF: 0.114 AC: 4745 AN: 41506

American (AMR) AF: 0.0530 AC: 810 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0605 AC: 210 AN: 3472

East Asian (EAS) AF: 0.00463 AC: 24 AN: 5182

South Asian (SAS) AF: 0.0553 AC: 267 AN: 4824

European-Finnish (FIN) AF: 0.0948 AC: 1005 AN: 10596

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0781 AC: 5314 AN: 68006

Other (OTH) AF: 0.0861 AC: 182 AN: 2114

Alfa AF: 0.0789 Hom.: 842

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
PhyloP100		-0.062
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: rs7565742; hg19: chr2-179244560;