Genetic Variant MIR205HG:n.671_679dupGCAGCAGCA (chr1-209432291-T-TAGCAGCAGC) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000366437.8(MIR205HG):n.671_679dupGCAGCAGCA 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 0.00071 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00019 ( 12 hom. )

Failed GnomAD Quality Control

Consequence

MIR205HG
ENST00000366437.8 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

Publications

10 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR205HG	NR_145433.1 link	n.617_625dupGCAGCAGCA	non_coding_transcript_exon_variant	Exon 3 of 3
MIR205HG	NR_145434.1 link	n.752_760dupGCAGCAGCA	non_coding_transcript_exon_variant	Exon 5 of 5
MIR205HG	NR_145435.1 link	n.700_708dupGCAGCAGCA	non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR205HG	ENST00000366437.8 link	n.671_679dupGCAGCAGCA	non_coding_transcript_exon_variant	Exon 4 of 4	3
MIR205HG	ENST00000429156.7 link	n.782_790dupGCAGCAGCA	non_coding_transcript_exon_variant	Exon 5 of 5	3
MIR205HG	ENST00000431096.7 link	n.703_711dupGCAGCAGCA	non_coding_transcript_exon_variant	Exon 4 of 4	3

Frequencies

GnomAD3 genomes

AF:

0.000682

AC:

102

AN:

149472

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00212

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000466

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000647

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000104

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000191

AC:

226

AN:

1183522

Hom.:

Cov.:

AF XY:

0.000212

AC XY:

124

AN XY:

585108

show subpopulations

African (AFR)

AF:

0.00290

AC:

AN:

25892

American (AMR)

AF:

0.000881

AC:

AN:

34058

Ashkenazi Jewish (ASJ)

AF:

0.0000614

AC:

AN:

16278

East Asian (EAS)

AF:

0.00

AC:

AN:

16402

South Asian (SAS)

AF:

0.000517

AC:

AN:

81278

European-Finnish (FIN)

AF:

0.0000333

AC:

AN:

30016

Middle Eastern (MID)

AF:

0.000240

AC:

AN:

4160

European-Non Finnish (NFE)

AF:

0.0000579

AC:

AN:

932542

Other (OTH)

AF:

0.000513

AC:

AN:

42896

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000709

AC:

106

AN:

149582

Hom.:

Cov.:

AF XY:

0.000740

AC XY:

AN XY:

72968

show subpopulations

African (AFR)

AF:

0.00221

AC:

AN:

40278

American (AMR)

AF:

0.000465

AC:

AN:

15046

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3456

East Asian (EAS)

AF:

0.00

AC:

AN:

5034

South Asian (SAS)

AF:

0.000648

AC:

AN:

4630

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10334

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.000104

AC:

AN:

67532

Other (OTH)

AF:

0.00

AC:

AN:

2080

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

2701

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.0

Splicing

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

Publications

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1-209432291-TAGCAGCAGCAGCAGCAGCAGCAGCAGC-TAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over