dbSNP rs2072136: OAS3:p.Ser567Ser (chr12-112961114-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_006187.4(OAS3):c.1701G>A(p.Ser567Ser) 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

Publications

32 publications found

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:

ENSG00000257452 (HGNC:):

ENSG00000257452 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
OAS3	NM_006187.4 link	c.1701G>A	p.Ser567Ser	synonymous_variant	Exon 8 of 16	ENST00000228928.12	NP_006178.2	Q9Y6K5
OAS3	NM_001410984.1 link	c.1701G>A	p.Ser567Ser	synonymous_variant	Exon 8 of 16		NP_001397913.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OAS3	ENST00000228928.12 link	c.1701G>A	p.Ser567Ser	synonymous_variant	Exon 8 of 16	1	NM_006187.4	ENSP00000228928.7		Q9Y6K5

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

GnomAD2 exomes

AF:

0.307

AC:

76067

AN:

248092

AF XY:

0.304

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 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

African (AFR)

AF:

0.0973

AC:

3256

AN:

33462

American (AMR)

AF:

0.369

AC:

16442

AN:

44598

Ashkenazi Jewish (ASJ)

AF:

0.157

AC:

4097

AN:

26126

East Asian (EAS)

AF:

0.648

AC:

25711

AN:

39674

South Asian (SAS)

AF:

0.372

AC:

32036

AN:

86174

European-Finnish (FIN)

AF:

0.373

AC:

19897

AN:

53352

Middle Eastern (MID)

AF:

0.180

AC:

1038

AN:

5766

European-Non Finnish (NFE)

AF:

0.231

AC:

256575

AN:

1111590

Other (OTH)

AF:

0.247

AC:

14887

AN:

60352

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

15059

30119

45178

60238

75297

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8940

17880

26820

35760

44700

<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:

0.233

AC:

35367

AN:

151716

Hom.:

5145

Cov.:

AF XY:

0.245

AC XY:

18141

AN XY:

74150

show subpopulations

African (AFR)

AF:

0.110

AC:

4513

AN:

41076

American (AMR)

AF:

0.276

AC:

4215

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.142

AC:

491

AN:

3468

East Asian (EAS)

AF:

0.657

AC:

3400

AN:

5174

South Asian (SAS)

AF:

0.383

AC:

1845

AN:

4820

European-Finnish (FIN)

AF:

0.372

AC:

3933

AN:

10576

Middle Eastern (MID)

AF:

0.150

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.240

AC:

16343

AN:

68000

Other (OTH)

AF:

0.234

AC:

493

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1307

2614

3922

5229

6536

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

382

764

1146

1528

1910

<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:

0.226

Hom.:

6739

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

(source)

DANN

Benign

0.80

PhyloP100

-1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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