chr2-178387618-C-T

Variant names:

• chr2-178387618-C-T
• rs10497516
• NM_032523.4:c.2156+479C>T

Variant summary

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

The NM_032523.4(OSBPL6):​c.2156+479C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.051 in 152,160 control chromosomes in the GnomAD database, including 301 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 0.051 (301 hom., cov: 32)
• Consequence: OSBPL6 NM_032523.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.828
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL6	NM_032523.4	c.2156+479C>T		intron_variant	Intron 20 of 24	ENST00000190611.9	NP_115912.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSBPL6	ENST00000190611.9	c.2156+479C>T		intron_variant	Intron 20 of 24	1	NM_032523.4	ENSP00000190611.4

Frequencies

GnomAD3 genomes AF: 0.0509 AC: 7734 AN: 152042 Hom.: 299 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0316

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.0288

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0265

Gnomad OTH AF: 0.0436

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

GnomAD4 genome AF: 0.0510 AC: 7755 AN: 152160 Hom.: 301 Cov.: 32 AF XY: 0.0492 AC XY: 3656 AN XY: 74380

African (AFR) AF: 0.101 AC: 4180 AN: 41492

American (AMR) AF: 0.0315 AC: 482 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0620 AC: 215 AN: 3470

East Asian (EAS) AF: 0.136 AC: 702 AN: 5178

South Asian (SAS) AF: 0.0294 AC: 142 AN: 4826

European-Finnish (FIN) AF: 0.0103 AC: 109 AN: 10592

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0265 AC: 1800 AN: 68006

Other (OTH) AF: 0.0446 AC: 94 AN: 2108

Alfa AF: 0.0414 Hom.: 52

Bravo AF: 0.0562

Asia WGS AF: 0.0870 AC: 301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	11
DANN	Benign	0.35
PhyloP100		0.83
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.15		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: rs10497516; hg19: chr2-179252345;