rs1555228618

Variant summary

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

The NM_002535.3(OAS2):​c.467G>A​(p.Ser156Asn) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

OAS2
NM_002535.3 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.172
Variant links:
Genes affected
OAS2 (HGNC:8087): (2'-5'-oligoadenylate synthetase 2) This gene encodes a member of the 2-5A synthetase family, essential proteins involved in the innate immune response to viral infection. The encoded protein is induced by interferons and uses adenosine triphosphate in 2'-specific nucleotidyl transfer reactions to synthesize 2',5'-oligoadenylates (2-5As). These molecules activate latent RNase L, which results in viral RNA degradation and the inhibition of viral replication. The three known members of this gene family are located in a cluster on chromosome 12. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

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=0.08200386).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OAS2NM_002535.3 linkc.467G>A p.Ser156Asn missense_variant Exon 3 of 10 ENST00000392583.7 NP_002526.2 P29728-2
OAS2NM_016817.3 linkc.467G>A p.Ser156Asn missense_variant Exon 3 of 11 NP_058197.2 P29728-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OAS2ENST00000392583.7 linkc.467G>A p.Ser156Asn missense_variant Exon 3 of 10 1 NM_002535.3 ENSP00000376362.3 P29728-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.15
BayesDel_addAF
Benign
-0.32
T
BayesDel_noAF
Benign
-0.70
CADD
Benign
14
DANN
Benign
0.77
DEOGEN2
Benign
0.029
T;.;.;T
Eigen
Benign
-0.46
Eigen_PC
Benign
-0.64
FATHMM_MKL
Benign
0.084
N
LIST_S2
Benign
0.38
T;T;T;T
M_CAP
Benign
0.0046
T
MetaRNN
Benign
0.082
T;T;T;T
MetaSVM
Benign
-0.99
T
MutationAssessor
Benign
0.94
L;L;.;.
PrimateAI
Benign
0.34
T
PROVEAN
Benign
-0.62
N;N;N;.
REVEL
Benign
0.086
Sift
Benign
1.0
T;T;T;.
Sift4G
Benign
0.25
T;T;T;T
Polyphen
1.0
D;D;.;.
Vest4
0.14
MutPred
0.48
Gain of catalytic residue at W158 (P = 0.0071);Gain of catalytic residue at W158 (P = 0.0071);.;Gain of catalytic residue at W158 (P = 0.0071);
MVP
0.37
MPC
0.23
ClinPred
0.099
T
GERP RS
2.0
Varity_R
0.023
gMVP
0.12

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: chr12-113433119; API