rs13311

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002535.3(OAS2):​c.*1592C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 160,106 control chromosomes in the GnomAD database, including 11,803 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.38 ( 11226 hom., cov: 30)
Exomes 𝑓: 0.32 ( 577 hom. )

Consequence

OAS2
NM_002535.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.606
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 Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OAS2NM_002535.3 linkuse as main transcriptc.*1592C>A 3_prime_UTR_variant 10/10 ENST00000392583.7
OAS2NM_016817.3 linkuse as main transcriptc.*363C>A 3_prime_UTR_variant 11/11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OAS2ENST00000392583.7 linkuse as main transcriptc.*1592C>A 3_prime_UTR_variant 10/101 NM_002535.3 P2P29728-2
ENST00000552784.1 linkuse as main transcriptn.353+6552G>T intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.381
AC:
57796
AN:
151662
Hom.:
11211
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.313
Gnomad AMI
AF:
0.536
Gnomad AMR
AF:
0.457
Gnomad ASJ
AF:
0.355
Gnomad EAS
AF:
0.517
Gnomad SAS
AF:
0.455
Gnomad FIN
AF:
0.427
Gnomad MID
AF:
0.351
Gnomad NFE
AF:
0.383
Gnomad OTH
AF:
0.373
GnomAD4 exome
AF:
0.319
AC:
2653
AN:
8326
Hom.:
577
Cov.:
0
AF XY:
0.315
AC XY:
1439
AN XY:
4562
show subpopulations
Gnomad4 AFR exome
AF:
0.295
Gnomad4 AMR exome
AF:
0.367
Gnomad4 ASJ exome
AF:
0.226
Gnomad4 EAS exome
AF:
0.463
Gnomad4 SAS exome
AF:
0.352
Gnomad4 FIN exome
AF:
0.384
Gnomad4 NFE exome
AF:
0.303
Gnomad4 OTH exome
AF:
0.325
GnomAD4 genome
AF:
0.381
AC:
57853
AN:
151780
Hom.:
11226
Cov.:
30
AF XY:
0.387
AC XY:
28692
AN XY:
74134
show subpopulations
Gnomad4 AFR
AF:
0.313
Gnomad4 AMR
AF:
0.457
Gnomad4 ASJ
AF:
0.355
Gnomad4 EAS
AF:
0.518
Gnomad4 SAS
AF:
0.455
Gnomad4 FIN
AF:
0.427
Gnomad4 NFE
AF:
0.383
Gnomad4 OTH
AF:
0.379
Alfa
AF:
0.383
Hom.:
15202
Bravo
AF:
0.379
Asia WGS
AF:
0.484
AC:
1682
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
8.8
DANN
Benign
0.68

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: rs13311; hg19: chr12-113448652; API