chr9-21425084-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000698343.1(MIR31HG):n.103-4392C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,014 control chromosomes in the GnomAD database, including 7,967 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 0.28 ( 7967 hom., cov: 32)
Consequence
MIR31HG
ENST00000698343.1 intron
ENST00000698343.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.858
Publications
1 publications found
Genes affected
MIR31HG (HGNC:37187): (MIR31 host gene) This gene produces a long non-coding RNA that acts as a host gene for miR-31. This transcript may be involved in cellular pluripotency and regulate the differentiation of myoblasts and other tissues. This RNA was found to interact with Polycomb repressive proteins to repression transcription of genes involves in cell senescence. [provided by RefSeq, Dec 2017]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|
Ensembl
Frequencies
GnomAD3 genomes AF: 0.283 AC: 42926AN: 151894Hom.: 7932 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
42926
AN:
151894
Hom.:
Cov.:
32
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 AF: 0.283 AC: 43017AN: 152014Hom.: 7967 Cov.: 32 AF XY: 0.281 AC XY: 20868AN XY: 74312 show subpopulations
GnomAD4 genome
AF:
AC:
43017
AN:
152014
Hom.:
Cov.:
32
AF XY:
AC XY:
20868
AN XY:
74312
show subpopulations
African (AFR)
AF:
AC:
21906
AN:
41460
American (AMR)
AF:
AC:
3668
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
AC:
582
AN:
3472
East Asian (EAS)
AF:
AC:
1363
AN:
5180
South Asian (SAS)
AF:
AC:
1495
AN:
4818
European-Finnish (FIN)
AF:
AC:
1742
AN:
10568
Middle Eastern (MID)
AF:
AC:
75
AN:
294
European-Non Finnish (NFE)
AF:
AC:
11568
AN:
67938
Other (OTH)
AF:
AC:
492
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1421
2843
4264
5686
7107
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
402
804
1206
1608
2010
<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.:
Bravo
AF:
Asia WGS
AF:
AC:
984
AN:
3478
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
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