chr9-21425084-G-A

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.858

Publications

1 publications found
Variant links:
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]

Genome browser will be placed here

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

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MIR31HGENST00000698343.1 linkn.103-4392C>T intron_variant Intron 1 of 4
MIR31HGENST00000698344.1 linkn.497-4392C>T intron_variant Intron 2 of 3
MIR31HGENST00000698345.1 linkn.255-4392C>T intron_variant Intron 2 of 2

Frequencies

GnomAD3 genomes
AF:
0.283
AC:
42926
AN:
151894
Hom.:
7932
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.528
Gnomad AMI
AF:
0.138
Gnomad AMR
AF:
0.241
Gnomad ASJ
AF:
0.168
Gnomad EAS
AF:
0.263
Gnomad SAS
AF:
0.310
Gnomad FIN
AF:
0.165
Gnomad MID
AF:
0.248
Gnomad NFE
AF:
0.170
Gnomad OTH
AF:
0.235
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.283
AC:
43017
AN:
152014
Hom.:
7967
Cov.:
32
AF XY:
0.281
AC XY:
20868
AN XY:
74312
show subpopulations
African (AFR)
AF:
0.528
AC:
21906
AN:
41460
American (AMR)
AF:
0.240
AC:
3668
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
0.168
AC:
582
AN:
3472
East Asian (EAS)
AF:
0.263
AC:
1363
AN:
5180
South Asian (SAS)
AF:
0.310
AC:
1495
AN:
4818
European-Finnish (FIN)
AF:
0.165
AC:
1742
AN:
10568
Middle Eastern (MID)
AF:
0.255
AC:
75
AN:
294
European-Non Finnish (NFE)
AF:
0.170
AC:
11568
AN:
67938
Other (OTH)
AF:
0.233
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:
0.231
Hom.:
652
Bravo
AF:
0.296
Asia WGS
AF:
0.283
AC:
984
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
1.0
DANN
Benign
0.59
PhyloP100
-0.86

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs7871767; hg19: chr9-21425083; API