NM_001126111.3:c.621-362G>C

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001126111.3(OSGIN2):​c.621-362G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSGIN2	NM_001126111.3	c.621-362G>C		intron_variant	Intron 5 of 5	ENST00000451899.7	NP_001119583.1
OSGIN2	NM_004337.2	c.489-362G>C		intron_variant	Intron 5 of 5		NP_004328.1
OSGIN2	XM_011517287.4	c.489-362G>C		intron_variant	Intron 5 of 5		XP_011515589.1
OSGIN2	XM_011517288.4	c.90-362G>C		intron_variant	Intron 2 of 2		XP_011515590.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSGIN2	ENST00000451899.7	c.621-362G>C		intron_variant	Intron 5 of 5	1	NM_001126111.3	ENSP00000396445.2
OSGIN2	ENST00000297438.6	c.489-362G>C		intron_variant	Intron 5 of 5	1		ENSP00000297438.2
OSGIN2	ENST00000647849.1	c.489-362G>C		intron_variant	Intron 5 of 5			ENSP00000497119.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 1081

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.61
PhyloP100		1.2

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;