rs2697677

Positions:

• chr8-89924141-G-A
• chr8-89924141-G-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSGIN2	NM_001126111.3	c.621-362G>A		intron_variant		ENST00000451899.7
OSGIN2	NM_004337.2	c.489-362G>A		intron_variant
OSGIN2	XM_011517287.4	c.489-362G>A		intron_variant
OSGIN2	XM_011517288.4	c.90-362G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSGIN2	ENST00000451899.7	c.621-362G>A		intron_variant		1	NM_001126111.3
OSGIN2	ENST00000297438.6	c.489-362G>A		intron_variant		1		P1
OSGIN2	ENST00000647849.1	c.489-362G>A		intron_variant				P1

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

Gnomad4 AFR AF: 0.0339

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.157

Alfa AF: 0.173 Hom.: 556

Bravo AF: 0.138

Asia WGS AF: 0.191 AC: 664 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.42

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

Publications

LitVar

Other links and lift over

dbSNP: rs2697677; hg19: chr8-90936369;