rs16882131

Variant names:

• chr6-52144135-C-T
• rs16882131
• ENST00000384872.3:n.-214C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_029713.1(MIR206):​n.-214C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,098 control chromosomes in the GnomAD database, including 5,493 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 0.27 (5493 hom., cov: 32)
• Consequence: MIR206 NR_029713.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.682

Genes affected

MIR206 (HGNC:31584): (microRNA 206) 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. Disruption of the encoded miRNA has been implicated in multiple skeletal muscle disorders, including amyotrophic lateral sclerosis (ALS) and Duchenne muscular dystrophy (DMD), as well as in several cancers. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR206	NR_029713.1	n.-214C>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR206	ENST00000384872.3	n.-214C>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40438 AN: 151980 Hom.: 5470 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.266 AC: 40507 AN: 152098 Hom.: 5493 Cov.: 32 AF XY: 0.265 AC XY: 19717 AN XY: 74346

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.274

Alfa AF: 0.274 Hom.: 3724

Bravo AF: 0.262

Asia WGS AF: 0.253 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.53
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16882131; hg19: chr6-52008933;