rs34479159

chr2-178239571-T-Cchr2-178239571-T-G

Variant summary

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

The NM_032523.4(OSBPL6):c.-351+44897T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 151,130 control chromosomes in the GnomAD database, including 2,412 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 0.16 (2412 hom., cov: 31)
• Consequence: OSBPL6 NM_032523.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL6	NM_032523.4	c.-351+44897T>C		intron_variant		ENST00000190611.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL6	ENST00000190611.9	c.-351+44897T>C		intron_variant		1	NM_032523.4	A1

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23927 AN: 151016 Hom.: 2411 Cov.: 31

Gnomad AFR AF: 0.0484

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0799

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.167

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.158 AC: 23931 AN: 151130 Hom.: 2412 Cov.: 31 AF XY: 0.163 AC XY: 12020 AN XY: 73780

Gnomad4 AFR AF: 0.0483

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.0804

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.165

Alfa AF: 0.168 Hom.: 760

Bravo AF: 0.139

Asia WGS AF: 0.160 AC: 556 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	7.0
Dann	Benign	0.48

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: rs34479159; hg19: chr2-179104298;