1-209432291-T-TAGCAGCAGCAGC

Position:

• chr1-209432291-T-TAGCAGCAGCAGC

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The ENST00000433108.1(MIR205HG):​n.3123_3134dupGCAGCAGCAGCA 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 0.00091 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00016 (13 hom.)
  • Failed GnomAD Quality Control
• Consequence: MIR205HG ENST00000433108.1 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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR205HG	NR_145433.1	n.614_625dupGCAGCAGCAGCA		non_coding_transcript_exon_variant	3/3
MIR205HG	NR_145434.1	n.749_760dupGCAGCAGCAGCA		non_coding_transcript_exon_variant	5/5
MIR205HG	NR_145435.1	n.697_708dupGCAGCAGCAGCA		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR205HG	ENST00000366437.7	n.475_486dupGCAGCAGCAGCA		non_coding_transcript_exon_variant	4/4	3
MIR205HG	ENST00000429156.6	n.776_787dupGCAGCAGCAGCA		non_coding_transcript_exon_variant	5/5	3
MIR205HG	ENST00000431096.6	n.697_708dupGCAGCAGCAGCA		non_coding_transcript_exon_variant	4/4	3

Frequencies

GnomAD3 genomes AF: 0.000890 AC: 133 AN: 149472 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00294

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000599

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: 0.0000296

Gnomad OTH AF: 0.00146

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000162 AC: 192 AN: 1183534 Hom.: 13 Cov.: 0 AF XY: 0.000166 AC XY: 97 AN XY: 585116

Gnomad4 AFR exome AF: 0.00409

Gnomad4 AMR exome AF: 0.000382

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000369

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000407

Gnomad4 OTH exome AF: 0.000676

GnomAD4 genome AF: 0.000909 AC: 136 AN: 149582 Hom.: 0 Cov.: 0 AF XY: 0.000850 AC XY: 62 AN XY: 72968

Gnomad4 AFR AF: 0.00300

Gnomad4 AMR AF: 0.000598

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000296

Gnomad4 OTH AF: 0.00144

Bravo AF: 0.00112

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;