rs2072136
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_006187.4(OAS3):c.1701G>A(p.Ser567=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 1,612,810 control chromosomes in the GnomAD database, including 58,973 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 0.23 ( 5145 hom., cov: 33)
Exomes 𝑓: 0.26 ( 53828 hom. )
Consequence
OAS3
NM_006187.4 synonymous
NM_006187.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.11
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP7
?
Synonymous conserved (PhyloP=-1.11 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OAS3 | NM_006187.4 | c.1701G>A | p.Ser567= | synonymous_variant | 8/16 | ENST00000228928.12 | |
OAS3 | NM_001410984.1 | c.1701G>A | p.Ser567= | synonymous_variant | 8/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OAS3 | ENST00000228928.12 | c.1701G>A | p.Ser567= | synonymous_variant | 8/16 | 1 | NM_006187.4 | P3 | |
ENST00000552784.1 | n.354-52436C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.233 AC: 35348AN: 151598Hom.: 5138 Cov.: 33
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GnomAD3 exomes AF: 0.307 AC: 76067AN: 248092Hom.: 13995 AF XY: 0.304 AC XY: 40976AN XY: 134582
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GnomAD4 exome AF: 0.256 AC: 373939AN: 1461094Hom.: 53828 Cov.: 35 AF XY: 0.259 AC XY: 188293AN XY: 726790
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GnomAD4 genome ? AF: 0.233 AC: 35367AN: 151716Hom.: 5145 Cov.: 33 AF XY: 0.245 AC XY: 18141AN XY: 74150
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at