rs1131476

Positions:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_016816.4(OAS1):c.1054G>A(p.Ala352Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 1,602,930 control chromosomes in the GnomAD database, including 374,330 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.75 ( 43990 hom., cov: 33)

Exomes 𝑓: 0.67 ( 330340 hom. )

Consequence

OAS1
NM_016816.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.117

Variant links:

Genes affected

OAS1 (HGNC:8086): (2'-5'-oligoadenylate synthetase 1) This interferon-induced gene encodes a protein that synthesizes 2',5'-oligoadenylates (2-5As). This protein plays a key role in innate cellular antiviral response, and has been implicated in other cellular processes like cell growth and apoptosis. Alternative splicing results in multiple transcript variants with different enzymatic activities. Polymorphisms in this gene have been associated with susceptibility to viral infection, including SARS-CoV-2, and diabetes mellitus, type 1. This gene is located in a cluster of related genes on chromosome 12. [provided by RefSeq, May 2022]

OAS1 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.1934328E-6).

BP6

Variant 12-112919404-G-A is Benign according to our data. Variant chr12-112919404-G-A is described in ClinVar as [Benign]. Clinvar id is 1167216.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OAS1	NM_016816.4 linkuse as main transcript	c.1054G>A	p.Ala352Thr	missense_variant	6/6	ENST00000202917.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OAS1	ENST00000202917.10 linkuse as main transcript	c.1054G>A	p.Ala352Thr	missense_variant	6/6	1	NM_016816.4	P2	P00973-1
	ENST00000552784.1 linkuse as main transcript	n.354-10726C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes

AF:

0.750

AC:

114022

AN:

152074

Hom.:

43924

Cov.:

show subpopulations

Gnomad AFR

AF:

0.930

Gnomad AMI

AF:

0.684

Gnomad AMR

AF:

0.767

Gnomad ASJ

AF:

0.500

Gnomad EAS

AF:

0.774

Gnomad SAS

AF:

0.708

Gnomad FIN

AF:

0.728

Gnomad MID

AF:

0.589

Gnomad NFE

AF:

0.657

Gnomad OTH

AF:

0.705

GnomAD3 exomes

AF:

0.715

AC:

178817

AN:

250208

Hom.:

65246

AF XY:

0.704

AC XY:

95211

AN XY:

135186

show subpopulations

Gnomad AFR exome

AF:

0.936

Gnomad AMR exome

AF:

0.827

Gnomad ASJ exome

AF:

0.507

Gnomad EAS exome

AF:

0.787

Gnomad SAS exome

AF:

0.693

Gnomad FIN exome

AF:

0.738

Gnomad NFE exome

AF:

0.659

Gnomad OTH exome

AF:

0.671

GnomAD4 exome

AF:

0.670

AC:

971906

AN:

1450738

Hom.:

330340

Cov.:

AF XY:

0.669

AC XY:

483124

AN XY:

722192

show subpopulations

Gnomad4 AFR exome

AF:

0.941

Gnomad4 AMR exome

AF:

0.820

Gnomad4 ASJ exome

AF:

0.512

Gnomad4 EAS exome

AF:

0.796

Gnomad4 SAS exome

AF:

0.693

Gnomad4 FIN exome

AF:

0.730

Gnomad4 NFE exome

AF:

0.651

Gnomad4 OTH exome

AF:

0.666

GnomAD4 genome

AF:

0.750

AC:

114152

AN:

152192

Hom.:

43990

Cov.:

AF XY:

0.752

AC XY:

55991

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.930

Gnomad4 AMR

AF:

0.767

Gnomad4 ASJ

AF:

0.500

Gnomad4 EAS

AF:

0.774

Gnomad4 SAS

AF:

0.709

Gnomad4 FIN

AF:

0.728

Gnomad4 NFE

AF:

0.657

Gnomad4 OTH

AF:

0.708

Alfa

AF:

0.664

Hom.:

59327

Bravo

AF:

0.763

TwinsUK

AF:

0.644

AC:

2388

ALSPAC

AF:

0.660

AC:

2543

ESP6500AA

AF:

0.923

AC:

4067

ESP6500EA

AF:

0.646

AC:

5555

ExAC

AF:

0.716

AC:

86959

Asia WGS

AF:

0.767

AC:

2666

AN:

3478

EpiCase

AF:

0.638

EpiControl

AF:

0.644

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 94% of patients studied by a panel of primary immunodeficiencies. Number of patients: 89. Only high quality variants are reported. -

OAS1-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

May 17, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.071

BayesDel_addAF

Benign

-0.83

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.21

DANN

Benign

0.89

DEOGEN2

Benign

0.023

T;T

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.010

LIST_S2

Benign

0.44

T;.

MetaRNN

Benign

0.0000012

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.0

N;.

MutationTaster

Benign

1.0

P;P;P

PrimateAI

Benign

0.23

PROVEAN

Benign

-0.26

N;.

REVEL

Benign

0.018

Sift

Benign

0.51

T;.

Sift4G

Benign

0.24

T;.

Polyphen

0.0020

B;.

Vest4

0.034

ClinPred

0.0058

GERP RS

-1.4

Varity_R

0.055

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over