chr16-83957702-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_182981.3(OSGIN1):ā€‹c.31G>Cā€‹(p.Ala11Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000934 in 1,605,868 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: š‘“ 0.0000066 ( 0 hom., cov: 32)
Exomes š‘“: 0.0000096 ( 0 hom. )

Consequence

OSGIN1
NM_182981.3 missense

Scores

1
18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.139
Variant links:
Genes affected
OSGIN1 (HGNC:30093): (oxidative stress induced growth inhibitor 1) This gene encodes an oxidative stress response protein that regulates cell death. Expression of the gene is regulated by p53 and is induced by DNA damage. The protein regulates apoptosis by inducing cytochrome c release from mitochondria. It also appears to be a key regulator of both inflammatory and anti-inflammatory molecules. The loss of this protein correlates with uncontrolled cell growth and tumor formation. Naturally occurring read-through transcription exists between this gene and the neighboring upstream malonyl-CoA decarboxylase (MLYCD) gene, but the read-through transcripts are unlikely to produce a protein product. [provided by RefSeq, Aug 2011]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.09872538).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OSGIN1NM_182981.3 linkc.31G>C p.Ala11Pro missense_variant Exon 2 of 6 ENST00000393306.6 NP_892026.1 Q9UJX0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OSGIN1ENST00000393306.6 linkc.31G>C p.Ala11Pro missense_variant Exon 2 of 6 1 NM_182981.3 ENSP00000376983.1 Q9UJX0

Frequencies

GnomAD3 genomes
AF:
0.00000658
AC:
1
AN:
151956
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000857
AC:
2
AN:
233440
Hom.:
0
AF XY:
0.0000158
AC XY:
2
AN XY:
126728
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000300
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000961
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000963
AC:
14
AN:
1453912
Hom.:
0
Cov.:
30
AF XY:
0.00000969
AC XY:
7
AN XY:
722626
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000228
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000118
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000993
Gnomad4 OTH exome
AF:
0.0000167
GnomAD4 genome
AF:
0.00000658
AC:
1
AN:
151956
Hom.:
0
Cov.:
32
AF XY:
0.0000135
AC XY:
1
AN XY:
74192
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000378
ExAC
AF:
0.00000828
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.078
BayesDel_addAF
Benign
-0.25
T
BayesDel_noAF
Benign
-0.51
CADD
Benign
2.9
DANN
Benign
0.96
DEOGEN2
Benign
0.00066
.;T;.;.;T
Eigen
Benign
-0.89
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.11
N
LIST_S2
Benign
0.60
.;T;T;T;T
M_CAP
Benign
0.047
D
MetaRNN
Benign
0.099
T;T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Uncertain
2.1
.;M;.;.;.
PrimateAI
Benign
0.33
T
PROVEAN
Benign
-0.92
N;N;N;.;N
REVEL
Benign
0.052
Sift
Benign
0.20
T;T;T;.;T
Sift4G
Benign
0.26
T;T;T;T;T
Polyphen
0.63
.;P;.;.;.
Vest4
0.29
MutPred
0.17
.;Gain of relative solvent accessibility (P = 0.0082);.;.;.;
MVP
0.36
MPC
0.25
ClinPred
0.080
T
GERP RS
-2.3
Varity_R
0.065
gMVP
0.47

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs781547435; hg19: chr16-83991307; API