20-44203039-C-T

Variant summary

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

The NM_016470.8(OSER1):​c.113G>A​(p.Gly38Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,262 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G38V) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

OSER1
NM_016470.8 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.266
Variant links:
Genes affected
OSER1 (HGNC:16105): (oxidative stress responsive serine rich 1) Predicted to be involved in cellular response to hydrogen peroxide. [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 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.085797906).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OSER1NM_016470.8 linkc.113G>A p.Gly38Asp missense_variant Exon 3 of 4 ENST00000255174.3 NP_057554.4 Q9NX31

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OSER1ENST00000255174.3 linkc.113G>A p.Gly38Asp missense_variant Exon 3 of 4 1 NM_016470.8 ENSP00000255174.2 Q9NX31
OSER1ENST00000372970.6 linkc.113G>A p.Gly38Asp missense_variant Exon 5 of 6 3 ENSP00000362061.1 Q9NX31

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.85e-7
AC:
1
AN:
1460262
Hom.:
0
Cov.:
28
AF XY:
0.00000138
AC XY:
1
AN XY:
726594
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:
9.00e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.16
BayesDel_addAF
Benign
-0.25
T
BayesDel_noAF
Benign
-0.60
CADD
Benign
15
DANN
Benign
0.96
DEOGEN2
Benign
0.013
T;T
Eigen
Benign
-0.67
Eigen_PC
Benign
-0.57
FATHMM_MKL
Benign
0.12
N
LIST_S2
Benign
0.78
.;T
M_CAP
Benign
0.0095
T
MetaRNN
Benign
0.086
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.0
N;N
PrimateAI
Benign
0.34
T
PROVEAN
Benign
0.14
N;N
REVEL
Benign
0.021
Sift
Benign
0.059
T;T
Sift4G
Benign
0.10
T;T
Polyphen
0.029
B;B
Vest4
0.30
MutPred
0.38
Loss of sheet (P = 0.0315);Loss of sheet (P = 0.0315);
MVP
0.15
MPC
0.21
ClinPred
0.14
T
GERP RS
1.6
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.088
gMVP
0.071

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: chr20-42831679; API