Variant chr9-21543445-A-G 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.51+16303T>C 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 0.109 in 151,986 control chromosomes in the GnomAD database, including 1,052 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 0.11 ( 1052 hom., cov: 32)

Consequence

MIR31HG
NR_152878.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.317

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:

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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=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
MIR31HG	NR_152878.1 linkuse as main transcript	n.51+16303T>C	intron_variant, non_coding_transcript_variant
MIR31HG	NR_027054.2 linkuse as main transcript	n.310+16044T>C	intron_variant, non_coding_transcript_variant
MIR31HG	NR_152877.1 linkuse as main transcript	n.51+16303T>C	intron_variant, non_coding_transcript_variant
MIR31HG	NR_152879.1 linkuse as main transcript	n.310+16044T>C	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR31HG	ENST00000698343.1 linkuse as main transcript	n.102+16303T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.109

AC:

16566

AN:

151868

Hom.:

1052

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0875

Gnomad AMI

AF:

0.0877

Gnomad AMR

AF:

0.124

Gnomad ASJ

AF:

0.100

Gnomad EAS

AF:

0.242

Gnomad SAS

AF:

0.262

Gnomad FIN

AF:

0.0976

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.0896

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.109

AC:

16576

AN:

151986

Hom.:

1052

Cov.:

AF XY:

0.113

AC XY:

8380

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.0875

Gnomad4 AMR

AF:

0.124

Gnomad4 ASJ

AF:

0.100

Gnomad4 EAS

AF:

0.242

Gnomad4 SAS

AF:

0.261

Gnomad4 FIN

AF:

0.0976

Gnomad4 NFE

AF:

0.101

Gnomad4 OTH

AF:

0.0900

Alfa

AF:

0.103

Hom.:

1308

Bravo

AF:

0.107

Asia WGS

AF:

0.183

AC:

636

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.7

DANN

Benign

0.38

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