Genetic Variant MIR31HG:n.604+5399G>A (chr9-21471500-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000304425.4(MIR31HG):n.604+5399G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 152,014 control chromosomes in the GnomAD database, including 28,011 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 0.60 ( 28011 hom., cov: 32)

Consequence

MIR31HG
ENST00000304425.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.18

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=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR31HG	NR_027054.2 link	n.571+5399G>A	intron_variant	Intron 3 of 3
MIR31HG	NR_152877.1 link	n.312+5399G>A	intron_variant	Intron 3 of 3
MIR31HG	NR_152878.1 link	n.175+5669G>A	intron_variant	Intron 2 of 2
MIR31HG	NR_152879.1 link	n.434+5669G>A	intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR31HG	ENST00000304425.4 link	n.604+5399G>A	intron_variant	Intron 3 of 3	2
MIR31HG	ENST00000654736.2 link	n.394+5399G>A	intron_variant	Intron 3 of 3
MIR31HG	ENST00000663833.2 link	n.246+5669G>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.603

AC:

91635

AN:

151896

Hom.:

27995

Cov.:

show subpopulations

Gnomad AFR

AF:

0.561

Gnomad AMI

AF:

0.621

Gnomad AMR

AF:

0.622

Gnomad ASJ

AF:

0.577

Gnomad EAS

AF:

0.921

Gnomad SAS

AF:

0.707

Gnomad FIN

AF:

0.570

Gnomad MID

AF:

0.614

Gnomad NFE

AF:

0.599

Gnomad OTH

AF:

0.608

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

GnomAD4 genome

AF:

0.603

AC:

91689

AN:

152014

Hom.:

28011

Cov.:

AF XY:

0.605

AC XY:

44975

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.561

Gnomad4 AMR

AF:

0.622

Gnomad4 ASJ

AF:

0.577

Gnomad4 EAS

AF:

0.920

Gnomad4 SAS

AF:

0.706

Gnomad4 FIN

AF:

0.570

Gnomad4 NFE

AF:

0.599

Gnomad4 OTH

AF:

0.612

Alfa

AF:

0.602

Hom.:

12579

Bravo

AF:

0.610

Asia WGS

AF:

0.793

AC:

2753

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.33

DANN

Benign

0.48

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