Variant chr9-21415688-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000669680.1(MIR31HG):n.5162+1138C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 152,034 control chromosomes in the GnomAD database, including 20,464 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 0.51 ( 20464 hom., cov: 32)

Consequence

MIR31HG
ENST00000669680.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.98

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 (AFR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect
MIR31HG	ENST00000669680.1 link	n.5162+1138C>T	intron_variant
MIR31HG	ENST00000698343.1 link	n.1404+2218C>T	intron_variant
MIR31HG	ENST00000698344.1 link	n.3283+2218C>T	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.510

AC:

77508

AN:

151916

Hom.:

20432

Cov.:

show subpopulations

Gnomad AFR

AF:

0.643

Gnomad AMI

AF:

0.453

Gnomad AMR

AF:

0.497

Gnomad ASJ

AF:

0.384

Gnomad EAS

AF:

0.562

Gnomad SAS

AF:

0.481

Gnomad FIN

AF:

0.485

Gnomad MID

AF:

0.465

Gnomad NFE

AF:

0.443

Gnomad OTH

AF:

0.480

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

GnomAD4 genome

AF:

0.510

AC:

77591

AN:

152034

Hom.:

20464

Cov.:

AF XY:

0.513

AC XY:

38120

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.643

Gnomad4 AMR

AF:

0.497

Gnomad4 ASJ

AF:

0.384

Gnomad4 EAS

AF:

0.563

Gnomad4 SAS

AF:

0.480

Gnomad4 FIN

AF:

0.485

Gnomad4 NFE

AF:

0.443

Gnomad4 OTH

AF:

0.482

Alfa

AF:

0.449

Hom.:

30850

Bravo

AF:

0.519

Asia WGS

AF:

0.524

AC:

1825

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.035

DANN

Benign

0.25

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