Genetic Variant ENST00000304425.4:n.604+5172G>A (chr9-21471727-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+5172G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 152,050 control chromosomes in the GnomAD database, including 18,175 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 0.48 ( 18175 hom., cov: 33)

Consequence

MIR31HG
ENST00000304425.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.18

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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR31HG	NR_027054.2 link	n.571+5172G>A	intron_variant	Intron 3 of 3
MIR31HG	NR_152877.1 link	n.312+5172G>A	intron_variant	Intron 3 of 3
MIR31HG	NR_152878.1 link	n.175+5442G>A	intron_variant	Intron 2 of 2
MIR31HG	NR_152879.1 link	n.434+5442G>A	intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR31HG	ENST00000304425.4 link	n.604+5172G>A	intron_variant	Intron 3 of 3	2
MIR31HG	ENST00000654736.2 link	n.394+5172G>A	intron_variant	Intron 3 of 3
MIR31HG	ENST00000663833.2 link	n.246+5442G>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.484

AC:

73482

AN:

151932

Hom.:

18169

Cov.:

show subpopulations

Gnomad AFR

AF:

0.390

Gnomad AMI

AF:

0.571

Gnomad AMR

AF:

0.495

Gnomad ASJ

AF:

0.519

Gnomad EAS

AF:

0.708

Gnomad SAS

AF:

0.472

Gnomad FIN

AF:

0.476

Gnomad MID

AF:

0.516

Gnomad NFE

AF:

0.519

Gnomad OTH

AF:

0.518

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

GnomAD4 genome

AF:

0.483

AC:

73499

AN:

152050

Hom.:

18175

Cov.:

AF XY:

0.484

AC XY:

35954

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.389

Gnomad4 AMR

AF:

0.495

Gnomad4 ASJ

AF:

0.519

Gnomad4 EAS

AF:

0.707

Gnomad4 SAS

AF:

0.471

Gnomad4 FIN

AF:

0.476

Gnomad4 NFE

AF:

0.519

Gnomad4 OTH

AF:

0.522

Alfa

AF:

0.524

Hom.:

41797

Bravo

AF:

0.490

Asia WGS

AF:

0.599

AC:

2082

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.56

DANN

Benign

0.17

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