rs2010549
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006187.4(OAS3):c.*1219G>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 0.181 in 152,312 control chromosomes in the GnomAD database, including 2,857 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 0.18 ( 2856 hom., cov: 33)
Exomes 𝑓: 0.19 ( 1 hom. )
Consequence
OAS3
NM_006187.4 3_prime_UTR
NM_006187.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.547
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]
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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=-0.87).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OAS3 | NM_006187.4 | c.*1219G>C | 3_prime_UTR_variant | 16/16 | ENST00000228928.12 | ||
OAS3 | NM_001410984.1 | c.*1219G>C | 3_prime_UTR_variant | 16/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OAS3 | ENST00000228928.12 | c.*1219G>C | 3_prime_UTR_variant | 16/16 | 1 | NM_006187.4 | P3 | ||
ENST00000552784.1 | n.353+46207C>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.181 AC: 27569AN: 152042Hom.: 2847 Cov.: 33
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GnomAD4 exome AF: 0.191 AC: 29AN: 152Hom.: 1 Cov.: 0 AF XY: 0.188 AC XY: 18AN XY: 96
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GnomAD4 genome ? AF: 0.181 AC: 27610AN: 152160Hom.: 2856 Cov.: 33 AF XY: 0.186 AC XY: 13868AN XY: 74386
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at