19-53725519-CTT-CTTT
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NR_030207.1(MIR516B2):n.81dupT 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 0.00000272 in 367,500 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
MIR516B2
NR_030207.1 non_coding_transcript_exon
NR_030207.1 non_coding_transcript_exon
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.286
Genes affected
MIR516B2 (HGNC:32117): (microRNA 516b-2) 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 Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MIR516B2 | NR_030207.1 | n.81dupT | non_coding_transcript_exon_variant | Exon 1 of 1 | ||||
MIR516B2 | unassigned_transcript_3367 | n.*41_*42insT | downstream_gene_variant | |||||
MIR516B2 | unassigned_transcript_3368 | n.*5_*6insT | downstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000413 AC: 1AN: 242356Hom.: 0 AF XY: 0.00000762 AC XY: 1AN XY: 131228
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GnomAD4 exome AF: 0.00000272 AC: 1AN: 367500Hom.: 0 Cov.: 0 AF XY: 0.00000481 AC XY: 1AN XY: 207756
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GnomAD4 genome Cov.: 32
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at