Variant rs11352835 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM4BP6BA1

The ENST00000540589.3(OAS1):c.1201del(p.Thr401ProfsTer26) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.74 ( 42993 hom., cov: 0)

Exomes 𝑓: 0.68 ( 127347 hom. )

Consequence

OAS1
ENST00000540589.3 frameshift

Scores

Not classified

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.554

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

PM4

Frameshift in the end of transcript resulting in stoplost. Downstream stopcodon found after 427 codons.

BP6

Variant 12-112931910-TA-T is Benign according to our data. Variant chr12-112931910-TA-T is described in ClinVar as [Benign]. Clinvar id is 3058877.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	Protein
OAS1	NM_001320151.2 linkuse as main transcript	c.1072del	p.Thr358ProfsTer26	frameshift_variant	6/6	NP_001307080.1
OAS1	NM_001406025.1 linkuse as main transcript	c.1048del	p.Thr350ProfsTer26	frameshift_variant	6/6	NP_001392954.1
OAS1	NR_175991.1 linkuse as main transcript	n.1377del		non_coding_transcript_exon_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	Protein	Appris	UniProt
OAS1	ENST00000540589.3 linkuse as main transcript	c.1201del	p.Thr401ProfsTer26	frameshift_variant	7/7	1	ENSP00000474083
OAS1	ENST00000551241.6 linkuse as main transcript	c.1072del	p.Thr358ProfsTer26	frameshift_variant	6/6	1	ENSP00000448790		P00973-4
OAS1	ENST00000552526.2 linkuse as main transcript	c.*30del		3_prime_UTR_variant	7/7	1	ENSP00000475139	A2
	ENST00000552784.1 linkuse as main transcript	n.354-23233del		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes

AF:

0.741

AC:

112568

AN:

151936

Hom.:

42934

Cov.:

show subpopulations

Gnomad AFR

AF:

0.927

Gnomad AMI

AF:

0.620

Gnomad AMR

AF:

0.750

Gnomad ASJ

AF:

0.499

Gnomad EAS

AF:

0.775

Gnomad SAS

AF:

0.709

Gnomad FIN

AF:

0.726

Gnomad MID

AF:

0.595

Gnomad NFE

AF:

0.644

Gnomad OTH

AF:

0.689

GnomAD3 exomes

AF:

0.699

AC:

95544

AN:

136774

Hom.:

34251

AF XY:

0.690

AC XY:

51071

AN XY:

74002

show subpopulations

Gnomad AFR exome

AF:

0.936

Gnomad AMR exome

AF:

0.809

Gnomad ASJ exome

AF:

0.500

Gnomad EAS exome

AF:

0.793

Gnomad SAS exome

AF:

0.691

Gnomad FIN exome

AF:

0.731

Gnomad NFE exome

AF:

0.636

Gnomad OTH exome

AF:

0.652

GnomAD4 exome

AF:

0.675

AC:

370471

AN:

548748

Hom.:

127347

Cov.:

AF XY:

0.672

AC XY:

199640

AN XY:

297064

show subpopulations

Gnomad4 AFR exome

AF:

0.923

Gnomad4 AMR exome

AF:

0.802

Gnomad4 ASJ exome

AF:

0.508

Gnomad4 EAS exome

AF:

0.802

Gnomad4 SAS exome

AF:

0.692

Gnomad4 FIN exome

AF:

0.724

Gnomad4 NFE exome

AF:

0.640

Gnomad4 OTH exome

AF:

0.670

GnomAD4 genome

AF:

0.741

AC:

112690

AN:

152054

Hom.:

42993

Cov.:

AF XY:

0.744

AC XY:

55301

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.927

Gnomad4 AMR

AF:

0.751

Gnomad4 ASJ

AF:

0.499

Gnomad4 EAS

AF:

0.775

Gnomad4 SAS

AF:

0.709

Gnomad4 FIN

AF:

0.726

Gnomad4 NFE

AF:

0.644

Gnomad4 OTH

AF:

0.692

Alfa

AF:

0.538

Hom.:

3183

Bravo

AF:

0.753

Asia WGS

AF:

0.768

AC:

2671

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

OAS1-related disorder

Benign:1

Benign, no assertion criteria provided

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

Splicing

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