5-160485411-C-G
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NR_029701.1(MIR146A):n.60C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 528,390 control chromosomes in the GnomAD database, including 141,782 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 0.70 ( 38097 hom., cov: 31)
Exomes 𝑓: 0.74 ( 103685 hom. )
Consequence
MIR146A
NR_029701.1 non_coding_transcript_exon
NR_029701.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.57
Genes affected
MIR3142HG (HGNC:51944): (MIR3142 host gene)
MIR146A (HGNC:31533): (microRNA 146a) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. Some of the targets of the encoded miRNA are the transcripts for tumor necrosis factor, interleukin 1 receptor-associated kinase 1, interleukin 1-beta, TNF receptor-associated factor 6, and complement factor H. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MIR146A | NR_029701.1 | n.60C>G | non_coding_transcript_exon_variant | 1/1 | |||
MIR3142HG | NR_132748.1 | n.303C>G | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIR3142HG | ENST00000517927.1 | n.286C>G | non_coding_transcript_exon_variant | 2/2 | 1 | ||||
MIR3142HG | ENST00000642173.1 | n.189C>G | non_coding_transcript_exon_variant | 2/2 | |||||
MIR146A | ENST00000385201.1 | n.60C>G | mature_miRNA_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.702 AC: 106630AN: 151942Hom.: 38071 Cov.: 31
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GnomAD3 exomes AF: 0.713 AC: 175623AN: 246292Hom.: 64108 AF XY: 0.719 AC XY: 95733AN XY: 133108
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GnomAD4 exome AF: 0.737 AC: 277348AN: 376330Hom.: 103685 Cov.: 0 AF XY: 0.738 AC XY: 157630AN XY: 213566
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GnomAD4 genome ? AF: 0.702 AC: 106701AN: 152060Hom.: 38097 Cov.: 31 AF XY: 0.702 AC XY: 52221AN XY: 74344
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at