dbSNP rs13311: OAS2:c.*1592C>A (chr12-113010847-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.606

Publications

22 publications found

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]

OAS2 links:

ENSG00000257452 (HGNC:):

ENSG00000257452 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
OAS2	NM_002535.3 link	c.*1592C>A		3_prime_UTR_variant	Exon 10 of 10	ENST00000392583.7	NP_002526.2	P29728-2
OAS2	NM_016817.3 link	c.*363C>A		3_prime_UTR_variant	Exon 11 of 11		NP_058197.2	P29728-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OAS2	ENST00000392583.7 link	c.*1592C>A		3_prime_UTR_variant	Exon 10 of 10	1	NM_002535.3	ENSP00000376362.3		P29728-2

Frequencies

GnomAD3 genomes

AF:

0.381

AC:

57796

AN:

151662

Hom.:

11211

Cov.:

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.:

AF XY:

0.315

AC XY:

1439

AN XY:

4562

show subpopulations

African (AFR)

AF:

0.295

AC:

AN:

156

American (AMR)

AF:

0.367

AC:

122

AN:

332

Ashkenazi Jewish (ASJ)

AF:

0.226

AC:

AN:

190

East Asian (EAS)

AF:

0.463

AC:

113

AN:

244

South Asian (SAS)

AF:

0.352

AC:

279

AN:

792

European-Finnish (FIN)

AF:

0.384

AC:

163

AN:

424

Middle Eastern (MID)

AF:

0.324

AC:

AN:

European-Non Finnish (NFE)

AF:

0.303

AC:

1725

AN:

5690

Other (OTH)

AF:

0.325

AC:

151

AN:

464

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

159

239

318

398

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.381

AC:

57853

AN:

151780

Hom.:

11226

Cov.:

AF XY:

0.387

AC XY:

28692

AN XY:

74134

show subpopulations

African (AFR)

AF:

0.313

AC:

12954

AN:

41382

American (AMR)

AF:

0.457

AC:

6959

AN:

15230

Ashkenazi Jewish (ASJ)

AF:

0.355

AC:

1230

AN:

3466

East Asian (EAS)

AF:

0.518

AC:

2662

AN:

5140

South Asian (SAS)

AF:

0.455

AC:

2178

AN:

4790

European-Finnish (FIN)

AF:

0.427

AC:

4494

AN:

10526

Middle Eastern (MID)

AF:

0.354

AC:

104

AN:

294

European-Non Finnish (NFE)

AF:

0.383

AC:

25985

AN:

67932

Other (OTH)

AF:

0.379

AC:

798

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1799

3598

5398

7197

8996

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

556

1112

1668

2224

2780

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.379

Hom.:

23052

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

(source)

DANN

Benign

0.68

PhyloP100

0.61

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over