Variant rs2072136 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_006187.4(OAS3):c.1701G>A(p.Ser567=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 1,612,810 control chromosomes in the GnomAD database, including 58,973 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 0.23 ( 5145 hom., cov: 33)

Exomes 𝑓: 0.26 ( 53828 hom. )

Consequence

OAS3
NM_006187.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.11

Variant links:

Genes affected

OAS3 (HGNC:8088): (2'-5'-oligoadenylate synthetase 3) This gene encodes an enzyme included in the 2', 5' oligoadenylate synthase family. This enzyme is induced by interferons and catalyzes the 2', 5' oligomers of adenosine in order to bind and activate RNase L. This enzyme family plays a significant role in the inhibition of cellular protein synthesis and viral infection resistance. [provided by RefSeq, Jul 2008]

OAS3 links:

(HGNC:):

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=-0.86).

BP7

Synonymous conserved (PhyloP=-1.11 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OAS3	NM_006187.4 linkuse as main transcript	c.1701G>A	p.Ser567=	synonymous_variant	8/16	ENST00000228928.12	NP_006178.2
OAS3	NM_001410984.1 linkuse as main transcript	c.1701G>A	p.Ser567=	synonymous_variant	8/16		NP_001397913.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OAS3	ENST00000228928.12 linkuse as main transcript	c.1701G>A	p.Ser567=	synonymous_variant	8/16	1	NM_006187.4	ENSP00000228928	P3
	ENST00000552784.1 linkuse as main transcript	n.354-52436C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes

AF:

0.233

AC:

35348

AN:

151598

Hom.:

5138

Cov.:

show subpopulations

Gnomad AFR

AF:

0.110

Gnomad AMI

AF:

0.0987

Gnomad AMR

AF:

0.275

Gnomad ASJ

AF:

0.142

Gnomad EAS

AF:

0.656

Gnomad SAS

AF:

0.383

Gnomad FIN

AF:

0.372

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.240

Gnomad OTH

AF:

0.234

GnomAD3 exomes

AF:

0.307

AC:

76067

AN:

248092

Hom.:

13995

AF XY:

0.304

AC XY:

40976

AN XY:

134582

show subpopulations

Gnomad AFR exome

AF:

0.106

Gnomad AMR exome

AF:

0.387

Gnomad ASJ exome

AF:

0.155

Gnomad EAS exome

AF:

0.669

Gnomad SAS exome

AF:

0.372

Gnomad FIN exome

AF:

0.375

Gnomad NFE exome

AF:

0.237

Gnomad OTH exome

AF:

0.261

GnomAD4 exome

AF:

0.256

AC:

373939

AN:

1461094

Hom.:

53828

Cov.:

AF XY:

0.259

AC XY:

188293

AN XY:

726790

show subpopulations

Gnomad4 AFR exome

AF:

0.0973

Gnomad4 AMR exome

AF:

0.369

Gnomad4 ASJ exome

AF:

0.157

Gnomad4 EAS exome

AF:

0.648

Gnomad4 SAS exome

AF:

0.372

Gnomad4 FIN exome

AF:

0.373

Gnomad4 NFE exome

AF:

0.231

Gnomad4 OTH exome

AF:

0.247

GnomAD4 genome

AF:

0.233

AC:

35367

AN:

151716

Hom.:

5145

Cov.:

AF XY:

0.245

AC XY:

18141

AN XY:

74150

show subpopulations

Gnomad4 AFR

AF:

0.110

Gnomad4 AMR

AF:

0.276

Gnomad4 ASJ

AF:

0.142

Gnomad4 EAS

AF:

0.657

Gnomad4 SAS

AF:

0.383

Gnomad4 FIN

AF:

0.372

Gnomad4 NFE

AF:

0.240

Gnomad4 OTH

AF:

0.234

Alfa

AF:

0.227

Hom.:

5529

Bravo

AF:

0.218

Asia WGS

AF:

0.428

AC:

1485

AN:

3478

EpiCase

AF:

0.219

EpiControl

AF:

0.210

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.1

DANN

Benign

0.80

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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