rs11352835
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM4BP6_ModerateBA1
The ENST00000540589.3(OAS1):βc.1201delβ(p.Thr401ProfsTer26) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (β ).
Frequency
Genomes: π 0.74 ( 42993 hom., cov: 0)
Exomes π: 0.68 ( 127347 hom. )
Consequence
OAS1
ENST00000540589.3 frameshift
ENST00000540589.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.554
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 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 criteria_provided_single_submitter, 1 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 | MANE | UniProt |
---|---|---|---|---|---|---|---|
OAS1 | NM_001320151.2 | c.1072del | p.Thr358ProfsTer26 | frameshift_variant | 6/6 | ||
OAS1 | NM_001406025.1 | c.1048del | p.Thr350ProfsTer26 | frameshift_variant | 6/6 | ||
OAS1 | NR_175991.1 | n.1377del | non_coding_transcript_exon_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OAS1 | ENST00000540589.3 | c.1201del | p.Thr401ProfsTer26 | frameshift_variant | 7/7 | 1 | |||
OAS1 | ENST00000551241.6 | c.1072del | p.Thr358ProfsTer26 | frameshift_variant | 6/6 | 1 | |||
OAS1 | ENST00000552526.2 | c.*30del | 3_prime_UTR_variant | 7/7 | 1 | A2 | |||
ENST00000552784.1 | n.354-23233del | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.741 AC: 112568AN: 151936Hom.: 42934 Cov.: 0
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GnomAD3 exomes AF: 0.699 AC: 95544AN: 136774Hom.: 34251 AF XY: 0.690 AC XY: 51071AN XY: 74002
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GnomAD4 exome AF: 0.675 AC: 370471AN: 548748Hom.: 127347 Cov.: 0 AF XY: 0.672 AC XY: 199640AN XY: 297064
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GnomAD4 genome ? AF: 0.741 AC: 112690AN: 152054Hom.: 42993 Cov.: 0 AF XY: 0.744 AC XY: 55301AN XY: 74304
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
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
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at