GeneBe

rs7849420

Positions:

Variant summary

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

The NR_152878.1(MIR31HG):​n.52-22333T>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 0.651 in 151,930 control chromosomes in the GnomAD database, including 32,669 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 0.65 ( 32669 hom., cov: 31)

Consequence

MIR31HG
NR_152878.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.348
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]

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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 (EAS) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MIR31HGNR_152878.1 linkuse as main transcriptn.52-22333T>G intron_variant, non_coding_transcript_variant
MIR31HGNR_027054.2 linkuse as main transcriptn.311-22333T>G intron_variant, non_coding_transcript_variant
MIR31HGNR_152877.1 linkuse as main transcriptn.52-22333T>G intron_variant, non_coding_transcript_variant
MIR31HGNR_152879.1 linkuse as main transcriptn.311-22333T>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MIR31HGENST00000698343.1 linkuse as main transcriptn.102+60123T>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.651
AC:
98898
AN:
151814
Hom.:
32670
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.574
Gnomad AMI
AF:
0.729
Gnomad AMR
AF:
0.692
Gnomad ASJ
AF:
0.656
Gnomad EAS
AF:
0.934
Gnomad SAS
AF:
0.772
Gnomad FIN
AF:
0.644
Gnomad MID
AF:
0.709
Gnomad NFE
AF:
0.658
Gnomad OTH
AF:
0.670
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.651
AC:
98927
AN:
151930
Hom.:
32669
Cov.:
31
AF XY:
0.655
AC XY:
48675
AN XY:
74264
show subpopulations
Gnomad4 AFR
AF:
0.573
Gnomad4 AMR
AF:
0.692
Gnomad4 ASJ
AF:
0.656
Gnomad4 EAS
AF:
0.934
Gnomad4 SAS
AF:
0.771
Gnomad4 FIN
AF:
0.644
Gnomad4 NFE
AF:
0.658
Gnomad4 OTH
AF:
0.674
Alfa
AF:
0.632
Hom.:
4115
Bravo
AF:
0.654
Asia WGS
AF:
0.818
AC:
2841
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
1.2
DANN
Benign
0.55

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: rs7849420; hg19: chr9-21499624; API