Variant 12-112987088-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_002535.3(OAS2):c.228C>G(p.Thr76Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 1,613,842 control chromosomes in the GnomAD database, including 62,659 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 0.26 ( 5479 hom., cov: 32)

Exomes 𝑓: 0.28 ( 57180 hom. )

Consequence

OAS2
NM_002535.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.609

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:

OAS2 (HGNC:):

OAS2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP7

Synonymous conserved (PhyloP=-0.609 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OAS2	NM_002535.3 linkuse as main transcript	c.228C>G	p.Thr76Thr	synonymous_variant	2/10	ENST00000392583.7	NP_002526.2	P29728-2
OAS2	NM_016817.3 linkuse as main transcript	c.228C>G	p.Thr76Thr	synonymous_variant	2/11		NP_058197.2	P29728-1
OAS2	NM_001032731.2 linkuse as main transcript	c.228C>G	p.Thr76Thr	synonymous_variant	2/2		NP_001027903.1	P29728-3Q7Z6D0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OAS2	ENST00000392583.7 linkuse as main transcript	c.228C>G	p.Thr76Thr	synonymous_variant	2/10	1	NM_002535.3	ENSP00000376362.3		P29728-2

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

39944

AN:

151908

Hom.:

5481

Cov.:

show subpopulations

Gnomad AFR

AF:

0.233

Gnomad AMI

AF:

0.443

Gnomad AMR

AF:

0.322

Gnomad ASJ

AF:

0.230

Gnomad EAS

AF:

0.0869

Gnomad SAS

AF:

0.217

Gnomad FIN

AF:

0.268

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.283

Gnomad OTH

AF:

0.257

GnomAD3 exomes

AF:

0.263

AC:

66092

AN:

251338

Hom.:

9282

AF XY:

0.260

AC XY:

35363

AN XY:

135836

show subpopulations

Gnomad AFR exome

AF:

0.234

Gnomad AMR exome

AF:

0.326

Gnomad ASJ exome

AF:

0.227

Gnomad EAS exome

AF:

0.0882

Gnomad SAS exome

AF:

0.222

Gnomad FIN exome

AF:

0.267

Gnomad NFE exome

AF:

0.289

Gnomad OTH exome

AF:

0.266

GnomAD4 exome

AF:

0.276

AC:

404040

AN:

1461816

Hom.:

57180

Cov.:

AF XY:

0.274

AC XY:

199146

AN XY:

727196

show subpopulations

Gnomad4 AFR exome

AF:

0.225

Gnomad4 AMR exome

AF:

0.329

Gnomad4 ASJ exome

AF:

0.231

Gnomad4 EAS exome

AF:

0.113

Gnomad4 SAS exome

AF:

0.221

Gnomad4 FIN exome

AF:

0.266

Gnomad4 NFE exome

AF:

0.289

Gnomad4 OTH exome

AF:

0.259

GnomAD4 genome

AF:

0.263

AC:

39956

AN:

152026

Hom.:

5479

Cov.:

AF XY:

0.261

AC XY:

19386

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.233

Gnomad4 AMR

AF:

0.322

Gnomad4 ASJ

AF:

0.230

Gnomad4 EAS

AF:

0.0863

Gnomad4 SAS

AF:

0.218

Gnomad4 FIN

AF:

0.268

Gnomad4 NFE

AF:

0.283

Gnomad4 OTH

AF:

0.254

Alfa

AF:

0.235

Hom.:

1427

Bravo

AF:

0.269

Asia WGS

AF:

0.176

AC:

618

AN:

3478

EpiCase

AF:

0.287

EpiControl

AF:

0.290

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.8

DANN

Benign

0.63

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over