3-67225635-G-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_036234.1(MIR4272):n.*108G>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.951 in 153,476 control chromosomes in the GnomAD database, including 69,502 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 0.95 ( 68957 hom., cov: 33)
Exomes 𝑓: 0.97 ( 545 hom. )
Consequence
MIR4272
NR_036234.1 downstream_gene
NR_036234.1 downstream_gene
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.670
Genes affected
MIR4272 (HGNC:38303): (microRNA 4272) 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=-0.98).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MIR4272 | NR_036234.1 | n.*108G>T | downstream_gene_variant | |||||
MIR4272 | unassigned_transcript_639 | n.*118G>T | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MIR4272 | ENST00000635924.1 | n.*108G>T | downstream_gene_variant | 6 |
Frequencies
GnomAD3 genomes AF: 0.951 AC: 144674AN: 152200Hom.: 68896 Cov.: 33
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GnomAD4 exome AF: 0.971 AC: 1123AN: 1156Hom.: 545 AF XY: 0.974 AC XY: 641AN XY: 658
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GnomAD4 genome AF: 0.951 AC: 144795AN: 152320Hom.: 68957 Cov.: 33 AF XY: 0.953 AC XY: 70948AN XY: 74470
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at