Genetic Variant MIR202HG:n.189G>A (chr10-133247608-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000300167.7(MIR202HG):n.189G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.779 in 459,196 control chromosomes in the GnomAD database, including 145,790 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 0.69 ( 40561 hom., cov: 33)

Exomes 𝑓: 0.82 ( 105229 hom. )

Consequence

MIR202HG
ENST00000300167.7 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.223

Variant links:

Genes affected

MIR202HG (HGNC:49402): (MIR202 host gene)

MIR202HG links:

MIR202 (HGNC:32080): (microRNA 202) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR202 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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR202	NR_030170.1 link	n.13G>A	non_coding_transcript_exon_variant	Exon 1 of 1
MIR202HG	NR_108078.1 link	n.189G>A	non_coding_transcript_exon_variant	Exon 2 of 3
MIR202HG	NR_108079.1 link	n.95+183G>A	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR202HG	ENST00000300167.7 link	n.189G>A	non_coding_transcript_exon_variant	Exon 2 of 3	2
MIR202	ENST00000362219.2 link	n.13G>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
MIR202HG	ENST00000553459.1 link	n.101+183G>A	intron_variant	Intron 1 of 1	2
MIR202HG	ENST00000669738.1 link	n.-73G>A	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.694

AC:

105402

AN:

151952

Hom.:

40550

Cov.:

show subpopulations

Gnomad AFR

AF:

0.334

Gnomad AMI

AF:

0.805

Gnomad AMR

AF:

0.722

Gnomad ASJ

AF:

0.764

Gnomad EAS

AF:

0.908

Gnomad SAS

AF:

0.811

Gnomad FIN

AF:

0.876

Gnomad MID

AF:

0.745

Gnomad NFE

AF:

0.848

Gnomad OTH

AF:

0.700

GnomAD3 exomes

AF:

0.800

AC:

123618

AN:

154602

Hom.:

50741

AF XY:

0.810

AC XY:

66136

AN XY:

81648

show subpopulations

Gnomad AFR exome

AF:

0.317

Gnomad AMR exome

AF:

0.742

Gnomad ASJ exome

AF:

0.759

Gnomad EAS exome

AF:

0.919

Gnomad SAS exome

AF:

0.818

Gnomad FIN exome

AF:

0.875

Gnomad NFE exome

AF:

0.849

Gnomad OTH exome

AF:

0.804

GnomAD4 exome

AF:

0.821

AC:

252238

AN:

307128

Hom.:

105229

Cov.:

AF XY:

0.824

AC XY:

143516

AN XY:

174078

show subpopulations

Gnomad4 AFR exome

AF:

0.329

Gnomad4 AMR exome

AF:

0.739

Gnomad4 ASJ exome

AF:

0.762

Gnomad4 EAS exome

AF:

0.918

Gnomad4 SAS exome

AF:

0.821

Gnomad4 FIN exome

AF:

0.879

Gnomad4 NFE exome

AF:

0.856

Gnomad4 OTH exome

AF:

0.793

GnomAD4 genome

AF:

0.693

AC:

105430

AN:

152068

Hom.:

40561

Cov.:

AF XY:

0.700

AC XY:

52057

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.333

Gnomad4 AMR

AF:

0.722

Gnomad4 ASJ

AF:

0.764

Gnomad4 EAS

AF:

0.908

Gnomad4 SAS

AF:

0.813

Gnomad4 FIN

AF:

0.876

Gnomad4 NFE

AF:

0.848

Gnomad4 OTH

AF:

0.703

Alfa

AF:

0.775

Hom.:

10104

Bravo

AF:

0.666

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.8

DANN

Benign

0.90

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