16-83965399-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_182981.3(OSGIN1):āc.826A>Gā(p.Thr276Ala) variant causes a missense 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. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 33)
Exomes š: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
OSGIN1
NM_182981.3 missense
NM_182981.3 missense
Scores
2
14
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.769
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=0.081051916).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OSGIN1 | NM_182981.3 | c.826A>G | p.Thr276Ala | missense_variant | 6/6 | ENST00000393306.6 | |
NECAB2 | XM_047434240.1 | c.-23+163A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OSGIN1 | ENST00000393306.6 | c.826A>G | p.Thr276Ala | missense_variant | 6/6 | 1 | NM_182981.3 | P1 | |
OSGIN1 | ENST00000361711.7 | c.826A>G | p.Thr276Ala | missense_variant | 6/6 | 2 | P1 | ||
OSGIN1 | ENST00000343939.6 | n.1458A>G | non_coding_transcript_exon_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1423934Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 704686
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1423934
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Cov.:
35
AF XY:
AC XY:
0
AN XY:
704686
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
M_CAP
Uncertain
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
D;T;D
Sift4G
Uncertain
D;D;D
Polyphen
0.0020
.;B;.
Vest4
MutPred
0.44
.;Loss of stability (P = 0.0325);.;
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
Score
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at