chr2-178380259-C-T

Position:

• chr2-178380259-C-T

Variant summary

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

The NM_032523.4(OSBPL6):​c.1534-2161C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 151,326 control chromosomes in the GnomAD database, including 6,152 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 0.25 (6152 hom., cov: 29)
• Consequence: OSBPL6 NM_032523.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.635

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL6	NM_032523.4	c.1534-2161C>T		intron_variant		ENST00000190611.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL6	ENST00000190611.9	c.1534-2161C>T		intron_variant		1	NM_032523.4	A1

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37822 AN: 151206 Hom.: 6151 Cov.: 29

Gnomad AFR AF: 0.0628

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.327

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.250 AC: 37822 AN: 151326 Hom.: 6152 Cov.: 29 AF XY: 0.256 AC XY: 18891 AN XY: 73860

Gnomad4 AFR AF: 0.0626

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.290

Alfa AF: 0.262 Hom.: 752

Bravo AF: 0.263

Asia WGS AF: 0.329 AC: 1144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1347297; hg19: chr2-179244986;