chr12-121033729-C-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_003733.4(OASL):c.213G>T(p.Gly71=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00107 in 1,612,684 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00085 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0011 ( 0 hom. )
Consequence
OASL
NM_003733.4 synonymous
NM_003733.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.180
Genes affected
OASL (HGNC:8090): (2'-5'-oligoadenylate synthetase like) Enables DNA binding activity and double-stranded RNA binding activity. Involved in several processes, including interleukin-27-mediated signaling pathway; negative regulation of viral genome replication; and positive regulation of RIG-I signaling pathway. Located in cytosol; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.33).
BP7
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Synonymous conserved (PhyloP=-0.18 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OASL | NM_003733.4 | c.213G>T | p.Gly71= | synonymous_variant | 2/6 | ENST00000257570.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OASL | ENST00000257570.10 | c.213G>T | p.Gly71= | synonymous_variant | 2/6 | 1 | NM_003733.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000854 AC: 130AN: 152162Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000955 AC: 239AN: 250308Hom.: 0 AF XY: 0.000968 AC XY: 131AN XY: 135400
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GnomAD4 exome AF: 0.00109 AC: 1592AN: 1460404Hom.: 0 Cov.: 33 AF XY: 0.00107 AC XY: 779AN XY: 726446
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GnomAD4 genome ? AF: 0.000854 AC: 130AN: 152280Hom.: 0 Cov.: 31 AF XY: 0.000725 AC XY: 54AN XY: 74456
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ClinVar
Not reported inComputational scores
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Benign
Cadd
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Dann
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at