rs9295535
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_049872.1(MIR5689):n.19T>C 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 0.2 in 147,136 control chromosomes in the GnomAD database, including 3,085 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 0.20 ( 3082 hom., cov: 23)
Exomes 𝑓: 0.20 ( 3 hom. )
Consequence
MIR5689
NR_049872.1 non_coding_transcript_exon
NR_049872.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.446
Genes affected
MIR5689 (HGNC:43479): (microRNA 5689) 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. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MIR5689 | NR_049872.1 | n.19T>C | non_coding_transcript_exon_variant | 1/1 | |||
MIR5689HG | NR_132993.1 | n.76+5331T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIR5689 | ENST00000581998.1 | n.19T>C | mature_miRNA_variant | 1/1 | |||||
MIR5689HG | ENST00000366312.2 | n.76+5331T>C | intron_variant, non_coding_transcript_variant | 3 | |||||
MIR5689HG | ENST00000449333.1 | n.89+5331T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.200 AC: 29338AN: 146954Hom.: 3085 Cov.: 23
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GnomAD3 exomes AF: 0.300 AC: 3AN: 10Hom.: 0 AF XY: 0.500 AC XY: 2AN XY: 4
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GnomAD4 exome AF: 0.200 AC: 12AN: 60Hom.: 3 Cov.: 0 AF XY: 0.250 AC XY: 6AN XY: 24
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GnomAD4 genome ? AF: 0.200 AC: 29345AN: 147076Hom.: 3082 Cov.: 23 AF XY: 0.201 AC XY: 14397AN XY: 71766
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at