chr1-209432291-T-TAGCAGC

Position:

• chr1-209432291-T-TAGCAGC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NR_145434.1(MIR205HG):​n.755_760dup variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0077 (12 hom., cov: 0)
  • Exomes 𝑓: 0.00093 (37 hom.)
• Consequence: MIR205HG NR_145434.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00774 (1158/149576) while in subpopulation AFR AF= 0.0268 (1079/40272). AF 95% confidence interval is 0.0255. There are 12 homozygotes in gnomad4. There are 504 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 12 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR205HG	NR_145434.1	n.755_760dup		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.634-347_634-342dup		intron_variant, non_coding_transcript_variant
MIR205	ENST00000384891.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.00768 AC: 1148 AN: 149466 Hom.: 12 Cov.: 0

Gnomad AFR AF: 0.0266

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00333

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.000252

Gnomad OTH AF: 0.00583

GnomAD3 exomes AF: 0.00171 AC: 333 AN: 194576 Hom.: 2 AF XY: 0.00152 AC XY: 160 AN XY: 105446

Gnomad AFR exome AF: 0.0215

Gnomad AMR exome AF: 0.00230

Gnomad ASJ exome AF: 0.000714

Gnomad EAS exome AF: 0.000338

Gnomad SAS exome AF: 0.000390

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000154

Gnomad OTH exome AF: 0.000203

GnomAD4 exome AF: 0.000929 AC: 1100 AN: 1183512 Hom.: 37 Cov.: 0 AF XY: 0.000863 AC XY: 505 AN XY: 585108

Gnomad4 AFR exome AF: 0.0292

Gnomad4 AMR exome AF: 0.00226

Gnomad4 ASJ exome AF: 0.000737

Gnomad4 EAS exome AF: 0.000305

Gnomad4 SAS exome AF: 0.000357

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000118

Gnomad4 OTH exome AF: 0.00224

GnomAD4 genome AF: 0.00774 AC: 1158 AN: 149576 Hom.: 12 Cov.: 0 AF XY: 0.00691 AC XY: 504 AN XY: 72964

Gnomad4 AFR AF: 0.0268

Gnomad4 AMR AF: 0.00332

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000252

Gnomad4 OTH AF: 0.00577

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;