GeneBe

rs10811561

Positions:

Variant summary

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

The NR_152878.1(MIR31HG):​n.51+29138C>T 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 0.571 in 149,430 control chromosomes in the GnomAD database, including 24,378 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 0.57 ( 24378 hom., cov: 31)

Consequence

MIR31HG
NR_152878.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.365
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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MIR31HGNR_152878.1 linkuse as main transcriptn.51+29138C>T intron_variant, non_coding_transcript_variant
MIR31HGNR_027054.2 linkuse as main transcriptn.310+28879C>T intron_variant, non_coding_transcript_variant
MIR31HGNR_152877.1 linkuse as main transcriptn.51+29138C>T intron_variant, non_coding_transcript_variant
MIR31HGNR_152879.1 linkuse as main transcriptn.310+28879C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MIR31HGENST00000698343.1 linkuse as main transcriptn.102+29138C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.571
AC:
85300
AN:
149314
Hom.:
24353
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.636
Gnomad AMI
AF:
0.697
Gnomad AMR
AF:
0.553
Gnomad ASJ
AF:
0.533
Gnomad EAS
AF:
0.655
Gnomad SAS
AF:
0.515
Gnomad FIN
AF:
0.522
Gnomad MID
AF:
0.568
Gnomad NFE
AF:
0.543
Gnomad OTH
AF:
0.586
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.571
AC:
85362
AN:
149430
Hom.:
24378
Cov.:
31
AF XY:
0.569
AC XY:
41630
AN XY:
73104
show subpopulations
Gnomad4 AFR
AF:
0.636
Gnomad4 AMR
AF:
0.553
Gnomad4 ASJ
AF:
0.533
Gnomad4 EAS
AF:
0.654
Gnomad4 SAS
AF:
0.514
Gnomad4 FIN
AF:
0.522
Gnomad4 NFE
AF:
0.543
Gnomad4 OTH
AF:
0.589
Alfa
AF:
0.557
Hom.:
46390
Bravo
AF:
0.590
Asia WGS
AF:
0.633
AC:
2200
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.2
DANN
Benign
0.33

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: rs10811561; hg19: chr9-21530609; API