rs9609078

Variant names:

• chr22-30757289-G-A
• rs9609078
• NM_030758.4:c.853+15920G>A

Your query was ambiguous. Multiple possible variants found:

• chr22-30757289-G-A
• chr22-30757289-G-T

Variant summary

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

The NM_030758.4(OSBP2):​c.853+15920G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 151,930 control chromosomes in the GnomAD database, including 3,763 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 0.18 (3763 hom., cov: 31)
• Consequence: OSBP2 NM_030758.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 6 publications found

Genes affected

OSBP2 (HGNC:8504): (oxysterol binding protein 2) The protein encoded by this gene contains a pleckstrin homology (PH) domain and an oxysterol-binding region. It binds oxysterols such as 7-ketocholesterol and may inhibit their cytotoxicity. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Sep 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBP2	NM_030758.4	c.853+15920G>A		intron_variant	Intron 2 of 13	ENST00000332585.11	NP_110385.1
OSBP2	NM_001282739.2	c.853+15920G>A		intron_variant	Intron 2 of 13		NP_001269668.1
OSBP2	NM_001282738.2	c.358+15920G>A		intron_variant	Intron 3 of 14		NP_001269667.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSBP2	ENST00000332585.11	c.853+15920G>A		intron_variant	Intron 2 of 13	1	NM_030758.4	ENSP00000332576.6

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28028 AN: 151812 Hom.: 3746 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0519

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.0603

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.185 AC: 28088 AN: 151930 Hom.: 3763 Cov.: 31 AF XY: 0.181 AC XY: 13459 AN XY: 74264

African (AFR) AF: 0.383 AC: 15852 AN: 41418

American (AMR) AF: 0.170 AC: 2590 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 449 AN: 3468

East Asian (EAS) AF: 0.0520 AC: 268 AN: 5156

South Asian (SAS) AF: 0.172 AC: 830 AN: 4818

European-Finnish (FIN) AF: 0.0603 AC: 636 AN: 10550

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7008 AN: 67962

Other (OTH) AF: 0.176 AC: 370 AN: 2102

Alfa AF: 0.123 Hom.: 2918

Bravo AF: 0.201

Asia WGS AF: 0.152 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.99
DANN	Benign	0.47
PhyloP100		0.23
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: rs9609078; hg19: chr22-31153276; COSMIC: COSV60252012;