rs10203141

Variant names:

• chr2-178325570-C-G
• rs10203141
• NM_032523.4:c.195+1301C>G

Your query was ambiguous. Multiple possible variants found:

• chr2-178325570-C-G
• chr2-178325570-C-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.195+1301C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 152,022 control chromosomes in the GnomAD database, including 8,996 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 0.32 (8996 hom., cov: 32)
• Consequence: OSBPL6 NM_032523.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL6	NM_032523.4	c.195+1301C>G		intron_variant	Intron 4 of 24	ENST00000190611.9	NP_115912.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSBPL6	ENST00000190611.9	c.195+1301C>G		intron_variant	Intron 4 of 24	1	NM_032523.4	ENSP00000190611.4

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48146 AN: 151906 Hom.: 8999 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.317 AC: 48147 AN: 152022 Hom.: 8996 Cov.: 32 AF XY: 0.319 AC XY: 23709 AN XY: 74294

African (AFR) AF: 0.118 AC: 4889 AN: 41474

American (AMR) AF: 0.297 AC: 4528 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1718 AN: 3472

East Asian (EAS) AF: 0.484 AC: 2505 AN: 5172

South Asian (SAS) AF: 0.352 AC: 1690 AN: 4806

European-Finnish (FIN) AF: 0.479 AC: 5058 AN: 10552

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.391 AC: 26583 AN: 67972

Other (OTH) AF: 0.343 AC: 726 AN: 2114

Alfa AF: 0.344 Hom.: 1290

Bravo AF: 0.295

Asia WGS AF: 0.418 AC: 1453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.66
PhyloP100		0.025
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: rs10203141; hg19: chr2-179190297;