5-88616114-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000502301.6(MIR9-2HG):n.217+54922G>A variant causes a intron change. 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 0.00040 ( 0 hom., cov: 17)
Consequence
MIR9-2HG
ENST00000502301.6 intron
ENST00000502301.6 intron
Scores
1
1
Clinical Significance
Not reported in ClinVar
Conservation
No conservation score assigned
Publications
1 publications found
Genes affected
MIR9-2HG (HGNC:42810): (MIR9-2 host gene) This is an evolutionarily conserved gene that produces alternatively spliced long non-coding RNAs that may be expressed predominantly in the brain and visual cortex. These transcripts may be involved in tumorigenesis, as depletion by siRNA suppressed glioma cell division. Transcripts may also bind to and regulate the activity of miR-411-5p and argonaut 2, thereby altering the expression of genes involved in tumor growth. [provided by RefSeq, Nov 2017]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MIR9-2HG | ENST00000502301.6 | n.217+54922G>A | intron_variant | Intron 3 of 4 | 4 | |||||
| MIR9-2HG | ENST00000506014.6 | n.151+54922G>A | intron_variant | Intron 2 of 3 | 4 | |||||
| MIR9-2HG | ENST00000506664.8 | n.107+62234G>A | intron_variant | Intron 1 of 2 | 2 |
Frequencies
GnomAD3 genomes 0.000396 AC: 30AN: 75710Hom.: 0 Cov.: 17 show subpopulations
GnomAD3 genomes
AF:
AC:
30
AN:
75710
Hom.:
Cov.:
17
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.000396 AC: 30AN: 75788Hom.: 0 Cov.: 17 AF XY: 0.000572 AC XY: 21AN XY: 36726 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
30
AN:
75788
Hom.:
Cov.:
17
AF XY:
AC XY:
21
AN XY:
36726
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
8
AN:
29144
American (AMR)
AF:
AC:
5
AN:
5484
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2002
East Asian (EAS)
AF:
AC:
1
AN:
2758
South Asian (SAS)
AF:
AC:
1
AN:
2780
European-Finnish (FIN)
AF:
AC:
2
AN:
3580
Middle Eastern (MID)
AF:
AC:
0
AN:
184
European-Non Finnish (NFE)
AF:
AC:
12
AN:
28474
Other (OTH)
AF:
AC:
1
AN:
1036
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000911322), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.392
Heterozygous variant carriers
0
2
4
6
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10
0.00
0.20
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0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
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6
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10
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>80
Age
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Uncertain
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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