ENST00000651138.2:n.382C>G
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000651138.2(MIR34BHG):n.382C>G 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 0.0000296 in 405,880 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000039 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000024 ( 0 hom. )
Consequence
MIR34BHG
ENST00000651138.2 non_coding_transcript_exon
ENST00000651138.2 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0940
Publications
17 publications found
Genes affected
MIR34BHG (HGNC:55987): (MIR34B and MIR34C host gene)
BTG4 (HGNC:13862): (BTG anti-proliferation factor 4) The protein encoded by this gene is a member of the BTG/Tob family. This family has structurally related proteins that appear to have antiproliferative properties. This encoded protein can induce G1 arrest in the cell cycle. [provided by RefSeq, Jul 2008]
MIR34B (HGNC:31636): (microRNA 34b) 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]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| MIR34BHG | NR_147706.1 | n.375C>G | non_coding_transcript_exon_variant | Exon 2 of 2 | ||||
| BTG4 | NM_001367974.1 | c.-27+1546G>C | intron_variant | Intron 1 of 4 | NP_001354903.1 | |||
| BTG4 | XM_024448589.2 | c.-27+1546G>C | intron_variant | Intron 1 of 7 | XP_024304357.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MIR34BHG | ENST00000651138.2 | n.382C>G | non_coding_transcript_exon_variant | Exon 2 of 2 | ||||||
| MIR34BHG | ENST00000726427.1 | n.489C>G | non_coding_transcript_exon_variant | Exon 3 of 3 | ||||||
| BTG4 | ENST00000689553.1 | c.-207-844G>C | intron_variant | Intron 1 of 6 | ENSP00000508793.1 | |||||
| MIR34B | ENST00000385076.3 | n.*100C>G | downstream_gene_variant | 6 |
Frequencies
GnomAD3 genomes 0.0000394 AC: 6AN: 152130Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
6
AN:
152130
Hom.:
Cov.:
33
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:
GnomAD4 exome AF: 0.0000236 AC: 6AN: 253750Hom.: 0 AF XY: 0.0000216 AC XY: 3AN XY: 138956 show subpopulations
GnomAD4 exome
AF:
AC:
6
AN:
253750
Hom.:
AF XY:
AC XY:
3
AN XY:
138956
show subpopulations
African (AFR)
AF:
AC:
0
AN:
6236
American (AMR)
AF:
AC:
0
AN:
20650
Ashkenazi Jewish (ASJ)
AF:
AC:
5
AN:
8174
East Asian (EAS)
AF:
AC:
0
AN:
7454
South Asian (SAS)
AF:
AC:
0
AN:
51076
European-Finnish (FIN)
AF:
AC:
0
AN:
25456
Middle Eastern (MID)
AF:
AC:
0
AN:
1036
European-Non Finnish (NFE)
AF:
AC:
0
AN:
122288
Other (OTH)
AF:
AC:
1
AN:
11380
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.0000394 AC: 6AN: 152130Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74314 show subpopulations
GnomAD4 genome
AF:
AC:
6
AN:
152130
Hom.:
Cov.:
33
AF XY:
AC XY:
2
AN XY:
74314
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41434
American (AMR)
AF:
AC:
0
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
AC:
5
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5184
South Asian (SAS)
AF:
AC:
0
AN:
4828
European-Finnish (FIN)
AF:
AC:
0
AN:
10600
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68012
Other (OTH)
AF:
AC:
0
AN:
2090
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.550
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
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
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.