Genetic Variant NM_006187.4:c.*1482T>C (chr12-112971455-T-C) – 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.*1482T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,514 control chromosomes in the GnomAD database, including 2,418 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 0.17 ( 2414 hom., cov: 33)

Exomes 𝑓: 0.21 ( 4 hom. )

Consequence

OAS3
NM_006187.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.31

Publications

17 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OAS3	NM_006187.4 link	c.*1482T>C		3_prime_UTR_variant	Exon 16 of 16	ENST00000228928.12	NP_006178.2
OAS3	NM_001410984.1 link	c.*1482T>C		3_prime_UTR_variant	Exon 16 of 16		NP_001397913.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OAS3	ENST00000228928.12 link	c.*1482T>C		3_prime_UTR_variant	Exon 16 of 16	1	NM_006187.4	ENSP00000228928.7

Frequencies

GnomAD3 genomes

AF:

0.173

AC:

26291

AN:

152070

Hom.:

2417

Cov.:

show subpopulations

Gnomad AFR

AF:

0.120

Gnomad AMI

AF:

0.155

Gnomad AMR

AF:

0.192

Gnomad ASJ

AF:

0.191

Gnomad EAS

AF:

0.324

Gnomad SAS

AF:

0.201

Gnomad FIN

AF:

0.205

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.181

Gnomad OTH

AF:

0.185

GnomAD4 exome

AF:

0.215

AC:

AN:

326

Hom.:

Cov.:

AF XY:

0.234

AC XY:

AN XY:

188

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.250

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.286

AC:

AN:

East Asian (EAS)

AF:

0.227

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.269

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.212

AC:

AN:

212

Other (OTH)

AF:

0.150

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.173

AC:

26297

AN:

152188

Hom.:

2414

Cov.:

AF XY:

0.176

AC XY:

13073

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.120

AC:

4994

AN:

41534

American (AMR)

AF:

0.192

AC:

2940

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.191

AC:

664

AN:

3470

East Asian (EAS)

AF:

0.325

AC:

1678

AN:

5168

South Asian (SAS)

AF:

0.200

AC:

964

AN:

4822

European-Finnish (FIN)

AF:

0.205

AC:

2170

AN:

10590

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.181

AC:

12302

AN:

67988

Other (OTH)

AF:

0.183

AC:

387

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1154

2308

3462

4616

5770

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

296

592

888

1184

1480

<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:

0.181

Hom.:

7341

Bravo

AF:

0.171

Asia WGS

AF:

0.207

AC:

718

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.90

(source)

DANN

Benign

0.67

PhyloP100

-1.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over