chr12-112931954-G-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000540589.3(OAS1):c.*32G>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 0.69 in 700,014 control chromosomes in the GnomAD database, including 170,199 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.74 ( 43022 hom., cov: 32)
Exomes 𝑓: 0.68 ( 127177 hom. )
Consequence
OAS1
ENST00000540589.3 3_prime_UTR
ENST00000540589.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.365
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 12-112931954-G-C is Benign according to our data. Variant chr12-112931954-G-C is described in ClinVar as [Benign]. Clinvar id is 2687938.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OAS1 | NM_001320151.2 | c.*32G>C | 3_prime_UTR_variant | 6/6 | |||
OAS1 | NM_001406025.1 | c.*32G>C | 3_prime_UTR_variant | 6/6 | |||
OAS1 | NR_175991.1 | n.1420G>C | non_coding_transcript_exon_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OAS1 | ENST00000540589.3 | c.*32G>C | 3_prime_UTR_variant | 7/7 | 1 | ||||
OAS1 | ENST00000551241.6 | c.*32G>C | 3_prime_UTR_variant | 6/6 | 1 | ||||
OAS1 | ENST00000552526.2 | c.*73G>C | 3_prime_UTR_variant | 7/7 | 1 | A2 | |||
ENST00000552784.1 | n.354-23276C>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.741 AC: 112619AN: 151962Hom.: 42963 Cov.: 32
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GnomAD3 exomes AF: 0.698 AC: 94770AN: 135748Hom.: 33956 AF XY: 0.690 AC XY: 50856AN XY: 73708
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GnomAD4 exome AF: 0.675 AC: 369964AN: 547934Hom.: 127177 Cov.: 0 AF XY: 0.672 AC XY: 199397AN XY: 296684
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GnomAD4 genome AF: 0.741 AC: 112741AN: 152080Hom.: 43022 Cov.: 32 AF XY: 0.745 AC XY: 55337AN XY: 74324
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 93% of patients studied by a panel of primary immunodeficiencies. Number of patients: 88. Only high quality variants are reported. - |
Computational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at