8-89924141-G-A

Variant names:

• chr8-89924141-G-A
• rs2697677
• NM_001126111.3:c.621-362G>A

Variant summary

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

The NM_001126111.3(OSGIN2):​c.621-362G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,106 control chromosomes in the GnomAD database, including 2,140 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 0.15 (2140 hom., cov: 32)
• Consequence: OSGIN2 NM_001126111.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 6 publications found

Genes affected

OSGIN2 (HGNC:1355): (oxidative stress induced growth inhibitor family member 2) Predicted to enable growth factor activity. Predicted to be involved in negative regulation of cell growth. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001126111.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSGIN2	NM_001126111.3	MANE Select	c.621-362G>A		intron	N/A	NP_001119583.1
	OSGIN2	NM_004337.2		c.489-362G>A		intron	N/A	NP_004328.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSGIN2	ENST00000451899.7	TSL:1 MANE Select	c.621-362G>A		intron	N/A	ENSP00000396445.2
	OSGIN2	ENST00000297438.6	TSL:1	c.489-362G>A		intron	N/A	ENSP00000297438.2
	OSGIN2	ENST00000647849.1		c.489-362G>A		intron	N/A	ENSP00000497119.1

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22331 AN: 151988 Hom.: 2136 Cov.: 32

Gnomad AFR AF: 0.0340

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.147 AC: 22343 AN: 152106 Hom.: 2140 Cov.: 32 AF XY: 0.150 AC XY: 11151 AN XY: 74352

African (AFR) AF: 0.0339 AC: 1409 AN: 41528

American (AMR) AF: 0.177 AC: 2711 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 409 AN: 3472

East Asian (EAS) AF: 0.261 AC: 1352 AN: 5174

South Asian (SAS) AF: 0.229 AC: 1104 AN: 4818

European-Finnish (FIN) AF: 0.203 AC: 2138 AN: 10548

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12610 AN: 67962

Other (OTH) AF: 0.157 AC: 332 AN: 2114

Alfa AF: 0.176 Hom.: 1081

Bravo AF: 0.138

Asia WGS AF: 0.191 AC: 664 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.42
PhyloP100		1.2
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: rs2697677; hg19: chr8-90936369;