rs72631833
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Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NR_029615.1(MIR183):n.51G>T variant causes a non coding transcript exon change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00199 in 529,310 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0051 ( 8 hom., cov: 33)
Exomes 𝑓: 0.00071 ( 1 hom. )
Consequence
MIR183
NR_029615.1 non_coding_transcript_exon
NR_029615.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Conservation
PhyloP100: 7.33
Genes affected
MIR183 (HGNC:31554): (microRNA 183) 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 -18 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.23).
BP6
?
Variant 7-129774964-C-A is Benign according to our data. Variant chr7-129774964-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 163973.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00514 (782/152278) while in subpopulation AFR AF= 0.0175 (727/41550). AF 95% confidence interval is 0.0164. There are 8 homozygotes in gnomad4. There are 359 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 8 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MIR183 | NR_029615.1 | n.51G>T | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIR183 | ENST00000384958.1 | n.51G>T | non_coding_transcript_exon_variant | 1/1 | |||||
ENST00000710872.1 | n.431+4826G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00512 AC: 779AN: 152160Hom.: 8 Cov.: 33
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GnomAD3 exomes AF: 0.00147 AC: 362AN: 245768Hom.: 3 AF XY: 0.00109 AC XY: 145AN XY: 133192
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GnomAD4 exome AF: 0.000713 AC: 269AN: 377032Hom.: 1 Cov.: 0 AF XY: 0.000580 AC XY: 124AN XY: 213952
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GnomAD4 genome ? AF: 0.00514 AC: 782AN: 152278Hom.: 8 Cov.: 33 AF XY: 0.00482 AC XY: 359AN XY: 74458
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Dec 20, 2012 | 51G>T in miR183: This variant has been identified in 0.5% individuals from the 1 000Genomes project (10/2000; rs72631833). It is also located in the loop region of the miRNA and is therefore unlikely to affect target binding specificity that is determined by the seed region. In summary, this variant is likely benign. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 13, 2019 | - - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at