Genetic Variant MIR4300HG:n.941-8546T>C (chr11-81890842-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000500502.5(MIR4300HG):n.941-8546T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0432 in 154,458 control chromosomes in the GnomAD database, including 158 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 0.043 ( 155 hom., cov: 32)

Exomes 𝑓: 0.051 ( 3 hom. )

Consequence

MIR4300HG
ENST00000500502.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.209

Variant links:

Genes affected

MIR4300HG (HGNC:52003): (MIR4300 host gene)

MIR4300HG links:

MIR4300 (HGNC:38184): (microRNA 4300) 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]

MIR4300 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=-0.91).

BA1

GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.051 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR4300HG	NR_120571.1 link	n.941-8546T>C	intron_variant	Intron 6 of 7
MIR4300	NR_036186.1 link	n.-6T>C	upstream_gene_variant
MIR4300	unassigned_transcript_1942	n.-74T>C	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR4300HG	ENST00000500502.5 link	n.941-8546T>C	intron_variant	Intron 6 of 7	1
MIR4300HG	ENST00000530896.6 link	n.473-8546T>C	intron_variant	Intron 3 of 4	3
MIR4300HG	ENST00000653173.1 link	n.419-65911T>C	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.0431

AC:

6535

AN:

151724

Hom.:

156

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0466

Gnomad AMI

AF:

0.179

Gnomad AMR

AF:

0.0380

Gnomad ASJ

AF:

0.0586

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0176

Gnomad FIN

AF:

0.0215

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0481

Gnomad OTH

AF:

0.0374

GnomAD3 exomes

AF:

0.0508

AC:

324

AN:

6382

Hom.:

AF XY:

0.0536

AC XY:

165

AN XY:

3078

show subpopulations

Gnomad AFR exome

AF:

0.0455

Gnomad AMR exome

AF:

0.0593

Gnomad ASJ exome

AF:

0.0510

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0185

Gnomad NFE exome

AF:

0.0523

Gnomad OTH exome

AF:

0.0486

GnomAD4 exome

AF:

0.0509

AC:

133

AN:

2614

Hom.:

Cov.:

AF XY:

0.0498

AC XY:

AN XY:

1346

show subpopulations

Gnomad4 AFR exome

AF:

0.0811

Gnomad4 AMR exome

AF:

0.125

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0532

Gnomad4 FIN exome

AF:

0.0235

Gnomad4 NFE exome

AF:

0.0385

Gnomad4 OTH exome

AF:

0.0258

GnomAD4 genome

AF:

0.0431

AC:

6543

AN:

151844

Hom.:

155

Cov.:

AF XY:

0.0406

AC XY:

3016

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.0467

Gnomad4 AMR

AF:

0.0379

Gnomad4 ASJ

AF:

0.0586

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0172

Gnomad4 FIN

AF:

0.0215

Gnomad4 NFE

AF:

0.0481

Gnomad4 OTH

AF:

0.0375

Alfa

AF:

0.0142

Hom.:

Bravo

AF:

0.0451

Asia WGS

AF:

0.0150

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.2

DANN

Benign

0.76

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