ENST00000384992.3:n.60G>A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The ENST00000384992.3(MIR222):n.60G>A 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 0.0000293 in 375,359 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. 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 0.000046 ( 0 hom., 2 hem., cov: 21)
Exomes 𝑓: 0.000022 ( 0 hom. 3 hem. )
Consequence
MIR222
ENST00000384992.3 non_coding_transcript_exon
ENST00000384992.3 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.639
Publications
13 publications found
Genes affected
MIR222 (HGNC:31602): (microRNA 222) 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 was made for transcript
Our verdict: Likely_benign. The variant received -6 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BS2
High Hemizygotes in GnomAd4 at 2 gene
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| MIR222 | NR_029636.1 | n.60G>A | non_coding_transcript_exon_variant | Exon 1 of 1 | ||||
| MIR222HG | NR_170290.1 | n.23071G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | ||||
| MIR222 | unassigned_transcript_3725 | n.-9G>A | upstream_gene_variant | |||||
| MIR222 | unassigned_transcript_3726 | n.*8G>A | downstream_gene_variant |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MIR222 | ENST00000384992.3 | n.60G>A | non_coding_transcript_exon_variant | Exon 1 of 1 | 6 | |||||
| MIR222HG | ENST00000688264.3 | n.539G>A | non_coding_transcript_exon_variant | Exon 4 of 4 | ||||||
| MIR222HG | ENST00000780204.1 | n.415G>A | non_coding_transcript_exon_variant | Exon 3 of 3 |
Frequencies
GnomAD3 genomes 0.0000370 AC: 4AN: 108187Hom.: 0 Cov.: 21 show subpopulations
GnomAD3 genomes
AF:
AC:
4
AN:
108187
Hom.:
Cov.:
21
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.0000355 AC: 6AN: 168870 AF XY: 0.0000534 show subpopulations
GnomAD2 exomes
AF:
AC:
6
AN:
168870
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000225 AC: 6AN: 267123Hom.: 0 Cov.: 0 AF XY: 0.0000289 AC XY: 3AN XY: 103669 show subpopulations
GnomAD4 exome
AF:
AC:
6
AN:
267123
Hom.:
Cov.:
0
AF XY:
AC XY:
3
AN XY:
103669
show subpopulations
African (AFR)
AF:
AC:
0
AN:
8257
American (AMR)
AF:
AC:
0
AN:
28129
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
8462
East Asian (EAS)
AF:
AC:
0
AN:
9632
South Asian (SAS)
AF:
AC:
1
AN:
38628
European-Finnish (FIN)
AF:
AC:
0
AN:
23745
Middle Eastern (MID)
AF:
AC:
0
AN:
1934
European-Non Finnish (NFE)
AF:
AC:
5
AN:
136245
Other (OTH)
AF:
AC:
0
AN:
12091
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.458
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Hom
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.0000462 AC: 5AN: 108236Hom.: 0 Cov.: 21 AF XY: 0.0000644 AC XY: 2AN XY: 31066 show subpopulations
GnomAD4 genome
AF:
AC:
5
AN:
108236
Hom.:
Cov.:
21
AF XY:
AC XY:
2
AN XY:
31066
show subpopulations
African (AFR)
AF:
AC:
1
AN:
29584
American (AMR)
AF:
AC:
0
AN:
10090
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2585
East Asian (EAS)
AF:
AC:
0
AN:
3436
South Asian (SAS)
AF:
AC:
0
AN:
2499
European-Finnish (FIN)
AF:
AC:
0
AN:
5694
Middle Eastern (MID)
AF:
AC:
0
AN:
212
European-Non Finnish (NFE)
AF:
AC:
4
AN:
51999
Other (OTH)
AF:
AC:
0
AN:
1467
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.450
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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