chr12-121033522-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_003733.4(OASL):c.420C>T(p.Ile140=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000654 in 1,614,160 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00077 ( 2 hom., cov: 31)
Exomes 𝑓: 0.00064 ( 7 hom. )
Consequence
OASL
NM_003733.4 synonymous
NM_003733.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.321
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 Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
?
Variant 12-121033522-G-A is Benign according to our data. Variant chr12-121033522-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2643403.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.321 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 2 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OASL | NM_003733.4 | c.420C>T | p.Ile140= | synonymous_variant | 2/6 | ENST00000257570.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OASL | ENST00000257570.10 | c.420C>T | p.Ile140= | synonymous_variant | 2/6 | 1 | NM_003733.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000769 AC: 117AN: 152156Hom.: 2 Cov.: 31
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GnomAD3 exomes AF: 0.00108 AC: 271AN: 250644Hom.: 2 AF XY: 0.00103 AC XY: 140AN XY: 135590
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GnomAD4 exome AF: 0.000642 AC: 938AN: 1461886Hom.: 7 Cov.: 31 AF XY: 0.000622 AC XY: 452AN XY: 727244
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GnomAD4 genome ? AF: 0.000768 AC: 117AN: 152274Hom.: 2 Cov.: 31 AF XY: 0.000793 AC XY: 59AN XY: 74440
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | OASL: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at