8-89902800-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001126111.3(OSGIN2):ā€‹c.7G>Cā€‹(p.Val3Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000251 in 1,194,634 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 0.0000025 ( 1 hom. )

Consequence

OSGIN2
NM_001126111.3 missense

Scores

3
4
9

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.49
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.3174292).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
OSGIN2NM_001126111.3 linkuse as main transcriptc.7G>C p.Val3Leu missense_variant 1/6 ENST00000451899.7 NP_001119583.1
OSGIN2NM_004337.2 linkuse as main transcriptc.-89+675G>C intron_variant NP_004328.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
OSGIN2ENST00000451899.7 linkuse as main transcriptc.7G>C p.Val3Leu missense_variant 1/61 NM_001126111.3 ENSP00000396445 Q9Y236-2
OSGIN2ENST00000297438.6 linkuse as main transcriptc.-89+675G>C intron_variant 1 ENSP00000297438 P1Q9Y236-1
OSGIN2ENST00000520659.1 linkuse as main transcriptc.7G>C p.Val3Leu missense_variant 1/52 ENSP00000431029
OSGIN2ENST00000647849.1 linkuse as main transcriptc.-89+889G>C intron_variant ENSP00000497119 P1Q9Y236-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000251
AC:
3
AN:
1194634
Hom.:
1
Cov.:
29
AF XY:
0.00000518
AC XY:
3
AN XY:
579230
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000312
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsDec 19, 2022The c.7G>C (p.V3L) alteration is located in exon 1 (coding exon 1) of the OSGIN2 gene. This alteration results from a G to C substitution at nucleotide position 7, causing the valine (V) at amino acid position 3 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.11
T
BayesDel_noAF
Benign
-0.40
CADD
Pathogenic
26
DANN
Uncertain
0.99
Eigen
Uncertain
0.29
Eigen_PC
Uncertain
0.26
FATHMM_MKL
Benign
0.76
D
LIST_S2
Benign
0.74
T;T
M_CAP
Pathogenic
0.47
D
MetaRNN
Benign
0.32
T;T
MetaSVM
Benign
-0.79
T
MutationTaster
Benign
1.0
D;N;N
PrimateAI
Pathogenic
0.80
T
PROVEAN
Benign
-0.32
N;N
REVEL
Benign
0.11
Sift
Uncertain
0.021
D;D
Sift4G
Pathogenic
0.0
D;D
Polyphen
1.0
D;.
Vest4
0.41
MutPred
0.24
Loss of sheet (P = 0.0357);Loss of sheet (P = 0.0357);
MVP
0.32
MPC
1.1
ClinPred
0.98
D
GERP RS
3.7
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
gMVP
0.29

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr8-90915028; API