Variant 1-209432291-TAGCAGCAGCAGCAGCAGCAGCAGCAGC-TAGCAGCAGCAGCAGCAGCAGCAGCAGCAGC details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000433108.1(MIR205HG):n.3132_3134dupGCA 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 0.069 ( 1124 hom., cov: 0)

Exomes 𝑓: 0.0093 ( 455 hom. )

Consequence

MIR205HG
ENST00000433108.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

Variant links:

Genes affected

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

MIR205HG links:

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]

MIR205 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
MIR205HG	NR_145433.1 link	n.623_625dupGCA	non_coding_transcript_exon_variant	3/3
MIR205HG	NR_145434.1 link	n.758_760dupGCA	non_coding_transcript_exon_variant	5/5
MIR205HG	NR_145435.1 link	n.706_708dupGCA	non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
MIR205HG	ENST00000366437.7 link	n.484_486dupGCA	non_coding_transcript_exon_variant	4/4	3
MIR205HG	ENST00000429156.6 link	n.785_787dupGCA	non_coding_transcript_exon_variant	5/5	3
MIR205HG	ENST00000431096.6 link	n.706_708dupGCA	non_coding_transcript_exon_variant	4/4	3

Frequencies

GnomAD3 genomes

AF:

0.0685

AC:

10235

AN:

149424

Hom.:

1121

Cov.:

show subpopulations

Gnomad AFR

AF:

0.230

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0326

Gnomad ASJ

AF:

0.0194

Gnomad EAS

AF:

0.0101

Gnomad SAS

AF:

0.0114

Gnomad FIN

AF:

0.000290

Gnomad MID

AF:

0.0287

Gnomad NFE

AF:

0.00329

Gnomad OTH

AF:

0.0554

GnomAD3 exomes

AF:

0.0172

AC:

3340

AN:

194576

Hom.:

127

AF XY:

0.0148

AC XY:

1558

AN XY:

105446

show subpopulations

Gnomad AFR exome

AF:

0.177

Gnomad AMR exome

AF:

0.0176

Gnomad ASJ exome

AF:

0.0181

Gnomad EAS exome

AF:

0.0114

Gnomad SAS exome

AF:

0.00803

Gnomad FIN exome

AF:

0.000348

Gnomad NFE exome

AF:

0.00333

Gnomad OTH exome

AF:

0.0229

GnomAD4 exome

AF:

0.00928

AC:

10980

AN:

1183418

Hom.:

455

Cov.:

AF XY:

0.00868

AC XY:

5080

AN XY:

585054

show subpopulations

Gnomad4 AFR exome

AF:

0.226

Gnomad4 AMR exome

AF:

0.0171

Gnomad4 ASJ exome

AF:

0.0186

Gnomad4 EAS exome

AF:

0.0137

Gnomad4 SAS exome

AF:

0.00791

Gnomad4 FIN exome

AF:

0.000666

Gnomad4 NFE exome

AF:

0.00258

Gnomad4 OTH exome

AF:

0.0196

GnomAD4 genome

AF:

0.0686

AC:

10259

AN:

149536

Hom.:

1124

Cov.:

AF XY:

0.0654

AC XY:

4773

AN XY:

72946

show subpopulations

Gnomad4 AFR

AF:

0.230

Gnomad4 AMR

AF:

0.0325

Gnomad4 ASJ

AF:

0.0194

Gnomad4 EAS

AF:

0.00993

Gnomad4 SAS

AF:

0.0108

Gnomad4 FIN

AF:

0.000290

Gnomad4 NFE

AF:

0.00329

Gnomad4 OTH

AF:

0.0548

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over