Variant 14-101041390-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_030582.1(MIR300):n.28C>T 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 0.496 in 533,582 control chromosomes in the GnomAD database, including 68,634 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 ( 20245 hom., cov: 32)

Exomes 𝑓: 0.49 ( 48389 hom. )

Consequence

MIR300
NR_030582.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.164

Variant links:

Genes affected

MIR300 (HGNC:33636): (microRNA 300) 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]

MIR300 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR300	NR_030582.1 linkuse as main transcript	n.28C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR300	ENST00000401138.1 linkuse as main transcript	n.28C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.506

AC:

76841

AN:

151932

Hom.:

20221

Cov.:

show subpopulations

Gnomad AFR

AF:

0.597

Gnomad AMI

AF:

0.545

Gnomad AMR

AF:

0.551

Gnomad ASJ

AF:

0.449

Gnomad EAS

AF:

0.762

Gnomad SAS

AF:

0.585

Gnomad FIN

AF:

0.495

Gnomad MID

AF:

0.516

Gnomad NFE

AF:

0.419

Gnomad OTH

AF:

0.508

GnomAD3 exomes

AF:

0.511

AC:

127914

AN:

250308

Hom.:

34489

AF XY:

0.505

AC XY:

68426

AN XY:

135508

show subpopulations

Gnomad AFR exome

AF:

0.601

Gnomad AMR exome

AF:

0.616

Gnomad ASJ exome

AF:

0.440

Gnomad EAS exome

AF:

0.771

Gnomad SAS exome

AF:

0.572

Gnomad FIN exome

AF:

0.504

Gnomad NFE exome

AF:

0.417

Gnomad OTH exome

AF:

0.474

GnomAD4 exome

AF:

0.492

AC:

187710

AN:

381532

Hom.:

48389

Cov.:

AF XY:

0.493

AC XY:

107163

AN XY:

217228

show subpopulations

Gnomad4 AFR exome

AF:

0.591

Gnomad4 AMR exome

AF:

0.618

Gnomad4 ASJ exome

AF:

0.440

Gnomad4 EAS exome

AF:

0.780

Gnomad4 SAS exome

AF:

0.561

Gnomad4 FIN exome

AF:

0.499

Gnomad4 NFE exome

AF:

0.422

Gnomad4 OTH exome

AF:

0.474

GnomAD4 genome

AF:

0.506

AC:

76917

AN:

152050

Hom.:

20245

Cov.:

AF XY:

0.513

AC XY:

38105

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.597

Gnomad4 AMR

AF:

0.552

Gnomad4 ASJ

AF:

0.449

Gnomad4 EAS

AF:

0.762

Gnomad4 SAS

AF:

0.584

Gnomad4 FIN

AF:

0.495

Gnomad4 NFE

AF:

0.419

Gnomad4 OTH

AF:

0.507

Alfa

AF:

0.454

Hom.:

7000

Bravo

AF:

0.513

Asia WGS

AF:

0.671

AC:

2329

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

8.3

DANN

Benign

0.36

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