chr1-209432291-TAGCAGCAGCAGCAGCAGC-T

Position:

• chr1-209432291-TAGCAGCAGCAGCAGCAGC-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NR_145434.1(MIR205HG):​n.743_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 0.0052 in 1,333,098 control chromosomes in the GnomAD database, including 29 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0047 (2 hom., cov: 0)
  • Exomes 𝑓: 0.0053 (27 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 Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR205HG	NR_145434.1	n.743_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.634-359_634-342del		intron_variant, non_coding_transcript_variant
MIR205	ENST00000384891.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.00474 AC: 709 AN: 149466 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.00172

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00473

Gnomad ASJ AF: 0.00145

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00194

Gnomad FIN AF: 0.0144

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00576

Gnomad OTH AF: 0.00632

GnomAD3 exomes AF: 0.00513 AC: 998 AN: 194576 Hom.: 6 AF XY: 0.00499 AC XY: 526 AN XY: 105446

Gnomad AFR exome AF: 0.00129

Gnomad AMR exome AF: 0.00375

Gnomad ASJ exome AF: 0.00345

Gnomad EAS exome AF: 0.0000676

Gnomad SAS exome AF: 0.00382

Gnomad FIN exome AF: 0.0139

Gnomad NFE exome AF: 0.00566

Gnomad OTH exome AF: 0.00670

GnomAD4 exome AF: 0.00525 AC: 6216 AN: 1183522 Hom.: 27 AF XY: 0.00515 AC XY: 3011 AN XY: 585108

Gnomad4 AFR exome AF: 0.00143

Gnomad4 AMR exome AF: 0.00332

Gnomad4 ASJ exome AF: 0.00307

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00380

Gnomad4 FIN exome AF: 0.0132

Gnomad4 NFE exome AF: 0.00536

Gnomad4 OTH exome AF: 0.00618

GnomAD4 genome AF: 0.00475 AC: 710 AN: 149576 Hom.: 2 Cov.: 0 AF XY: 0.00506 AC XY: 369 AN XY: 72964

Gnomad4 AFR AF: 0.00171

Gnomad4 AMR AF: 0.00472

Gnomad4 ASJ AF: 0.00145

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00216

Gnomad4 FIN AF: 0.0144

Gnomad4 NFE AF: 0.00576

Gnomad4 OTH AF: 0.00625

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;