NM_032523.4:c.-351+44897T>C

Variant names:

• chr2-178239571-T-C
• rs34479159
• NM_032523.4:c.-351+44897T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032523.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL6	NM_032523.4	MANE Select	c.-351+44897T>C		intron	N/A	NP_115912.1	Q9BZF3-1
	OSBPL6	NM_001201480.2		c.-351+44897T>C		intron	N/A	NP_001188409.1	Q9BZF3-5
	OSBPL6	NM_001201481.2		c.-351+44897T>C		intron	N/A	NP_001188410.1	Q9BZF3-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL6	ENST00000190611.9	TSL:1 MANE Select	c.-351+44897T>C		intron	N/A	ENSP00000190611.4	Q9BZF3-1
	OSBPL6	ENST00000392505.6	TSL:1	c.-351+44897T>C		intron	N/A	ENSP00000376293.2	Q9BZF3-5
	OSBPL6	ENST00000357080.8	TSL:1	c.-351+44897T>C		intron	N/A	ENSP00000349591.4	Q9BZF3-6

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

African (AFR) AF: 0.0483 AC: 1989 AN: 41170

American (AMR) AF: 0.126 AC: 1911 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 477 AN: 3458

East Asian (EAS) AF: 0.0804 AC: 415 AN: 5160

South Asian (SAS) AF: 0.230 AC: 1104 AN: 4796

European-Finnish (FIN) AF: 0.285 AC: 2910 AN: 10208

Middle Eastern (MID) AF: 0.214 AC: 62 AN: 290

European-Non Finnish (NFE) AF: 0.214 AC: 14505 AN: 67866

Other (OTH) AF: 0.165 AC: 346 AN: 2092

Alfa AF: 0.158 Hom.: 798

Bravo AF: 0.139

Asia WGS AF: 0.160 AC: 556 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.0
DANN	Benign	0.48
PhyloP100		0.21
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: rs34479159; hg19: chr2-179104298;