rs141277168

Variant summary

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

The NM_002535.3(OAS2):​c.665C>A​(p.Pro222Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,792 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

OAS2
NM_002535.3 missense

Scores

1
18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.14
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=0.14582205).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OAS2NM_002535.3 linkc.665C>A p.Pro222Gln missense_variant Exon 4 of 10 ENST00000392583.7 NP_002526.2 P29728-2
OAS2NM_016817.3 linkc.665C>A p.Pro222Gln missense_variant Exon 4 of 11 NP_058197.2 P29728-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OAS2ENST00000392583.7 linkc.665C>A p.Pro222Gln missense_variant Exon 4 of 10 1 NM_002535.3 ENSP00000376362.3 P29728-2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251114
Hom.:
0
AF XY:
0.00000737
AC XY:
1
AN XY:
135700
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461792
Hom.:
0
Cov.:
31
AF XY:
0.00000138
AC XY:
1
AN XY:
727200
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
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
0.14
BayesDel_addAF
Benign
-0.38
T
BayesDel_noAF
Benign
-0.61
CADD
Benign
0.010
DANN
Benign
0.64
DEOGEN2
Benign
0.042
T;.;.;T
Eigen
Benign
-1.3
Eigen_PC
Benign
-1.4
FATHMM_MKL
Benign
0.016
N
LIST_S2
Benign
0.51
T;T;T;T
M_CAP
Benign
0.0037
T
MetaRNN
Benign
0.15
T;T;T;T
MetaSVM
Benign
-0.99
T
MutationAssessor
Benign
0.10
N;N;.;.
PrimateAI
Benign
0.22
T
PROVEAN
Benign
-0.98
N;N;N;.
REVEL
Benign
0.058
Sift
Benign
0.29
T;T;T;.
Sift4G
Uncertain
0.051
T;T;T;D
Polyphen
0.87
P;B;.;.
Vest4
0.12
MutPred
0.59
Gain of catalytic residue at L217 (P = 0.0037);Gain of catalytic residue at L217 (P = 0.0037);.;Gain of catalytic residue at L217 (P = 0.0037);
MVP
0.23
MPC
0.16
ClinPred
0.13
T
GERP RS
-7.6
Varity_R
0.022
gMVP
0.14

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

LitVar

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

Other links and lift over

dbSNP: rs141277168; hg19: chr12-113435362; COSMIC: COSV60804760; COSMIC: COSV60804760; API