1-209432291-TAGCAGCAGCAGCAGCAGCAGCAGCAGC-TAGCAGCAGCAGCAGC

Position:

• chr1-209432291-TAGCAGCAGCAGCAGCAGCAGCAGCAGC-TAGCAGCAGCAGCAGC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NR_145434.1(MIR205HG):​n.749_760del 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 0.618 in 1,332,644 control chromosomes in the GnomAD database, including 259,280 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.53 (24311 hom., cov: 0)
  • Exomes 𝑓: 0.63 (234969 hom.)
• Consequence: MIR205HG NR_145434.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.825

Genes affected

MIR205HG (HGNC:43562): (MIR205 host gene)

MIR205 (HGNC:31583): (microRNA 205) 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

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR205HG	NR_145434.1	n.749_760del		non_coding_transcript_exon_variant	5/5
MIR205	NR_029622.1			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR205HG	ENST00000657184.2	n.634-353_634-342del		intron_variant, non_coding_transcript_variant
MIR205	ENST00000384891.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.534 AC: 79665 AN: 149280 Hom.: 24300 Cov.: 0

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.554

GnomAD3 exomes AF: 0.602 AC: 117179 AN: 194576 Hom.: 36454 AF XY: 0.605 AC XY: 63842 AN XY: 105446

Gnomad AFR exome AF: 0.177

Gnomad AMR exome AF: 0.668

Gnomad ASJ exome AF: 0.675

Gnomad EAS exome AF: 0.706

Gnomad SAS exome AF: 0.613

Gnomad FIN exome AF: 0.605

Gnomad NFE exome AF: 0.605

Gnomad OTH exome AF: 0.604

GnomAD4 exome AF: 0.629 AC: 744513 AN: 1183254 Hom.: 234969 AF XY: 0.628 AC XY: 367623 AN XY: 584962

Gnomad4 AFR exome AF: 0.166

Gnomad4 AMR exome AF: 0.660

Gnomad4 ASJ exome AF: 0.676

Gnomad4 EAS exome AF: 0.701

Gnomad4 SAS exome AF: 0.619

Gnomad4 FIN exome AF: 0.595

Gnomad4 NFE exome AF: 0.642

Gnomad4 OTH exome AF: 0.609

GnomAD4 genome AF: 0.533 AC: 79696 AN: 149390 Hom.: 24311 Cov.: 0 AF XY: 0.540 AC XY: 39331 AN XY: 72858

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.559

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3842530; hg19: chr1-209605636;