ENST00000401138.1:n.28C>T

Variant names:

• chr14-101041390-C-T
• rs12894467
• ENST00000401138.1:n.28C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000401138.1(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 ENST00000401138.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 35 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000401138.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR300	NR_030582.1		n.28C>T		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR300	ENST00000401138.1	TSL:6	n.28C>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76841 AN: 151932 Hom.: 20221 Cov.: 32

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

GnomAD2 exomes AF: 0.511 AC: 127914 AN: 250308 AF XY: 0.505

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 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.: 0 AF XY: 0.493 AC XY: 107163 AN XY: 217228

African (AFR) AF: 0.591 AC: 6196 AN: 10482

American (AMR) AF: 0.618 AC: 22381 AN: 36214

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 5137 AN: 11686

East Asian (EAS) AF: 0.780 AC: 10247 AN: 13132

South Asian (SAS) AF: 0.561 AC: 37356 AN: 66600

European-Finnish (FIN) AF: 0.499 AC: 16055 AN: 32188

Middle Eastern (MID) AF: 0.531 AC: 1513 AN: 2850

European-Non Finnish (NFE) AF: 0.422 AC: 80910 AN: 191690

Other (OTH) AF: 0.474 AC: 7915 AN: 16690

GnomAD4 genome AF: 0.506 AC: 76917 AN: 152050 Hom.: 20245 Cov.: 32 AF XY: 0.513 AC XY: 38105 AN XY: 74314

African (AFR) AF: 0.597 AC: 24775 AN: 41466

American (AMR) AF: 0.552 AC: 8432 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1558 AN: 3468

East Asian (EAS) AF: 0.762 AC: 3933 AN: 5164

South Asian (SAS) AF: 0.584 AC: 2819 AN: 4830

European-Finnish (FIN) AF: 0.495 AC: 5226 AN: 10568

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28451 AN: 67960

Other (OTH) AF: 0.507 AC: 1071 AN: 2112

Alfa AF: 0.459 Hom.: 29235

Bravo AF: 0.513

Asia WGS AF: 0.671 AC: 2329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.3
DANN	Benign	0.36
PhyloP100		-0.16

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12894467; hg19: chr14-101507727; COSMIC: COSV62999658;