rs2384072
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000540589.3(OAS1):c.1168-2261T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 152,138 control chromosomes in the GnomAD database, including 43,390 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 0.74 ( 43390 hom., cov: 32)
Consequence
OAS1
ENST00000540589.3 intron
ENST00000540589.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.237
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OAS1 | NM_001320151.2 | c.1039-2261T>C | intron_variant | ||||
OAS1 | NM_001406025.1 | c.1015-2261T>C | intron_variant | ||||
OAS1 | NR_175991.1 | n.1344-2261T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OAS1 | ENST00000540589.3 | c.1168-2261T>C | intron_variant | 1 | |||||
OAS1 | ENST00000551241.6 | c.1039-2261T>C | intron_variant | 1 | |||||
OAS1 | ENST00000552526.2 | c.1083-2261T>C | intron_variant | 1 | A2 | ||||
ENST00000552784.1 | n.354-20939A>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.744 AC: 113048AN: 152020Hom.: 43326 Cov.: 32
GnomAD3 genomes
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32
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GnomAD4 genome ? AF: 0.744 AC: 113176AN: 152138Hom.: 43390 Cov.: 32 AF XY: 0.747 AC XY: 55550AN XY: 74386
GnomAD4 genome
?
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32
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55550
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74386
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2675
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at