Variant 12-113010483-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM4BA1

The NM_016817.3(OAS2):c.2159A>G(p.Ter720Trpext*?) variant causes a stop lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 1,612,108 control chromosomes in the GnomAD database, including 391,934 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 0.77 ( 46180 hom., cov: 31)

Exomes 𝑓: 0.68 ( 345754 hom. )

Consequence

OAS2
NM_016817.3 stop_lost

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0320

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 Likely_benign. Variant got -6 ACMG points.

PM4

Stoplost variant in NM_016817.3 Downstream stopcodon found after 749 codons.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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.*1228A>G		3_prime_UTR_variant	10/10	ENST00000392583.7	NP_002526.2	P29728-2
OAS2	NM_016817.3 linkuse as main transcript	c.2159A>G	p.Ter720Trpext*?	stop_lost	11/11		NP_058197.2	P29728-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OAS2	ENST00000392583.7 linkuse as main transcript	c.*1228A>G		3_prime_UTR_variant	10/10	1	NM_002535.3	ENSP00000376362.3		P29728-2

Frequencies

GnomAD3 genomes

AF:

0.767

AC:

116656

AN:

152028

Hom.:

46114

Cov.:

show subpopulations

Gnomad AFR

AF:

0.938

Gnomad AMI

AF:

0.593

Gnomad AMR

AF:

0.764

Gnomad ASJ

AF:

0.547

Gnomad EAS

AF:

0.994

Gnomad SAS

AF:

0.819

Gnomad FIN

AF:

0.774

Gnomad MID

AF:

0.589

Gnomad NFE

AF:

0.658

Gnomad OTH

AF:

0.722

GnomAD3 exomes

AF:

0.751

AC:

187410

AN:

249656

Hom.:

72231

AF XY:

0.742

AC XY:

100121

AN XY:

134970

show subpopulations

Gnomad AFR exome

AF:

0.944

Gnomad AMR exome

AF:

0.828

Gnomad ASJ exome

AF:

0.554

Gnomad EAS exome

AF:

0.997

Gnomad SAS exome

AF:

0.806

Gnomad FIN exome

AF:

0.784

Gnomad NFE exome

AF:

0.659

Gnomad OTH exome

AF:

0.695

GnomAD4 exome

AF:

0.682

AC:

996301

AN:

1459962

Hom.:

345754

Cov.:

AF XY:

0.684

AC XY:

496706

AN XY:

726268

show subpopulations

Gnomad4 AFR exome

AF:

0.948

Gnomad4 AMR exome

AF:

0.820

Gnomad4 ASJ exome

AF:

0.553

Gnomad4 EAS exome

AF:

0.989

Gnomad4 SAS exome

AF:

0.803

Gnomad4 FIN exome

AF:

0.779

Gnomad4 NFE exome

AF:

0.647

Gnomad4 OTH exome

AF:

0.694

GnomAD4 genome

AF:

0.768

AC:

116786

AN:

152146

Hom.:

46180

Cov.:

AF XY:

0.774

AC XY:

57587

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.938

Gnomad4 AMR

AF:

0.765

Gnomad4 ASJ

AF:

0.547

Gnomad4 EAS

AF:

0.994

Gnomad4 SAS

AF:

0.818

Gnomad4 FIN

AF:

0.774

Gnomad4 NFE

AF:

0.658

Gnomad4 OTH

AF:

0.724

Alfa

AF:

0.668

Hom.:

80676

Bravo

AF:

0.775

TwinsUK

AF:

0.635

AC:

2356

ALSPAC

AF:

0.648

AC:

2497

ESP6500AA

AF:

0.933

AC:

4112

ESP6500EA

AF:

0.656

AC:

5639

ExAC

AF:

0.753

AC:

91467

Asia WGS

AF:

0.901

AC:

3131

AN:

3478

EpiCase

AF:

0.637

EpiControl

AF:

0.636

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.82

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.5

DANN

Benign

0.72

Eigen

Benign

0.11

Eigen_PC

Benign

-0.29

FATHMM_MKL

Benign

0.093

GERP RS

0.85

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.

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