Variant chr9-21499625-A-C details in Genebe, Genetics Data Aggregator

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

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]

MIR31HG links:

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
MIR31HG	NR_152878.1 linkuse as main transcript	n.52-22333T>G	intron_variant, non_coding_transcript_variant
MIR31HG	NR_027054.2 linkuse as main transcript	n.311-22333T>G	intron_variant, non_coding_transcript_variant
MIR31HG	NR_152877.1 linkuse as main transcript	n.52-22333T>G	intron_variant, non_coding_transcript_variant
MIR31HG	NR_152879.1 linkuse as main transcript	n.311-22333T>G	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000698343.1 linkuse as main transcript	n.102+60123T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.651

AC:

98898

AN:

151814

Hom.:

32670

Cov.:

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.:

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over