9-21428771-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000698343.1(MIR31HG):​n.103-8079A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,272 control chromosomes in the GnomAD database, including 1,317 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 0.13 ( 1317 hom., cov: 33)

Consequence

MIR31HG
ENST00000698343.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.37
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MIR31HGENST00000698343.1 linkuse as main transcriptn.103-8079A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.129
AC:
19688
AN:
152154
Hom.:
1315
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.135
Gnomad AMI
AF:
0.253
Gnomad AMR
AF:
0.139
Gnomad ASJ
AF:
0.134
Gnomad EAS
AF:
0.114
Gnomad SAS
AF:
0.109
Gnomad FIN
AF:
0.136
Gnomad MID
AF:
0.146
Gnomad NFE
AF:
0.123
Gnomad OTH
AF:
0.124
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.129
AC:
19687
AN:
152272
Hom.:
1317
Cov.:
33
AF XY:
0.130
AC XY:
9679
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.135
Gnomad4 AMR
AF:
0.138
Gnomad4 ASJ
AF:
0.134
Gnomad4 EAS
AF:
0.114
Gnomad4 SAS
AF:
0.109
Gnomad4 FIN
AF:
0.136
Gnomad4 NFE
AF:
0.123
Gnomad4 OTH
AF:
0.122
Alfa
AF:
0.129
Hom.:
1176
Bravo
AF:
0.131
Asia WGS
AF:
0.143
AC:
496
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.53
DANN
Benign
0.62

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7043990; hg19: chr9-21428770; API