rs10583889
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NR_030207.1(MIR516B2):n.80_81del 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 0.00955 in 519,700 control chromosomes in the GnomAD database, including 218 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.025 ( 169 hom., cov: 32)
Exomes 𝑓: 0.0033 ( 49 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 Benign. Variant got -8 ACMG points.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0838 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MIR516B2 | NR_030207.1 | n.80_81del | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIR516B2 | ENST00000385190.1 | n.80_81del | non_coding_transcript_exon_variant | 1/1 | |||||
ENST00000710708.1 | n.585+12420_585+12421del | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0246 AC: 3736AN: 152106Hom.: 167 Cov.: 32
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GnomAD3 exomes AF: 0.00391 AC: 948AN: 242356Hom.: 36 AF XY: 0.00260 AC XY: 341AN XY: 131228
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GnomAD4 exome AF: 0.00328 AC: 1206AN: 367476Hom.: 49 AF XY: 0.00243 AC XY: 504AN XY: 207750
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GnomAD4 genome ? AF: 0.0247 AC: 3756AN: 152224Hom.: 169 Cov.: 32 AF XY: 0.0236 AC XY: 1758AN XY: 74426
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ClinVar
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at