dbSNP rs2240189: OAS3:c.2404-52G>A (chr12-112965692-G-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_006187.4(OAS3):c.2404-52G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 1,541,466 control chromosomes in the GnomAD database, including 53,531 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 0.24 ( 4486 hom., cov: 33)

Exomes 𝑓: 0.26 ( 49045 hom. )

Consequence

OAS3
NM_006187.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.341

Publications

13 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006187.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OAS3	NM_006187.4	MANE Select	c.2404-52G>A		intron	N/A	NP_006178.2
	OAS3	NM_001410984.1		c.2404-205G>A		intron	N/A	NP_001397913.1	A0A7P0T8S7

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
OAS3	ENST00000228928.12	TSL:1 MANE Select	c.2404-52G>A	intron	N/A	ENSP00000228928.7	Q9Y6K5
OAS3	ENST00000679493.1		c.2404-52G>A	intron	N/A	ENSP00000506397.1	A0A7P0TAU8
OAS3	ENST00000681346.1		c.2404-52G>A	intron	N/A	ENSP00000505939.1	A0A7P0Z4F1

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

35784

AN:

152062

Hom.:

4487

Cov.:

show subpopulations

Gnomad AFR

AF:

0.160

Gnomad AMI

AF:

0.419

Gnomad AMR

AF:

0.307

Gnomad ASJ

AF:

0.208

Gnomad EAS

AF:

0.157

Gnomad SAS

AF:

0.196

Gnomad FIN

AF:

0.264

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.269

Gnomad OTH

AF:

0.217

GnomAD4 exome

AF:

0.262

AC:

364551

AN:

1389286

Hom.:

49045

AF XY:

0.260

AC XY:

177949

AN XY:

685094

show subpopulations

African (AFR)

AF:

0.152

AC:

4905

AN:

32282

American (AMR)

AF:

0.316

AC:

12374

AN:

39102

Ashkenazi Jewish (ASJ)

AF:

0.201

AC:

4846

AN:

24118

East Asian (EAS)

AF:

0.172

AC:

6507

AN:

37934

South Asian (SAS)

AF:

0.196

AC:

15362

AN:

78484

European-Finnish (FIN)

AF:

0.259

AC:

9994

AN:

38604

Middle Eastern (MID)

AF:

0.203

AC:

826

AN:

4066

European-Non Finnish (NFE)

AF:

0.275

AC:

295677

AN:

1076874

Other (OTH)

AF:

0.243

AC:

14060

AN:

57822

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

14117

28234

42352

56469

70586

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10024

20048

30072

40096

50120

<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:

0.235

AC:

35799

AN:

152180

Hom.:

4486

Cov.:

AF XY:

0.235

AC XY:

17504

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.160

AC:

6653

AN:

41514

American (AMR)

AF:

0.306

AC:

4686

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.208

AC:

722

AN:

3466

East Asian (EAS)

AF:

0.156

AC:

811

AN:

5186

South Asian (SAS)

AF:

0.197

AC:

950

AN:

4818

European-Finnish (FIN)

AF:

0.264

AC:

2794

AN:

10592

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.269

AC:

18289

AN:

67994

Other (OTH)

AF:

0.214

AC:

453

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1438

2875

4313

5750

7188

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

364

728

1092

1456

1820

<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:

0.246

Hom.:

1032

Bravo

AF:

0.239

Asia WGS

AF:

0.196

AC:

683

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.0

(source)

DANN

Benign

0.66

PhyloP100

-0.34

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over