Genetic Variant MIR205HG:n.665_679dupGCAGCAGCAGCAGCA (chr1-209432291-T-TAGCAGCAGCAGCAGC) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The ENST00000366437.8(MIR205HG):n.665_679dupGCAGCAGCAGCAGCA variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00044 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000053 ( 4 hom. )

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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAdExome4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR205HG	NR_145433.1 link	n.611_625dupGCAGCAGCAGCAGCA	non_coding_transcript_exon_variant	Exon 3 of 3
MIR205HG	NR_145434.1 link	n.746_760dupGCAGCAGCAGCAGCA	non_coding_transcript_exon_variant	Exon 5 of 5
MIR205HG	NR_145435.1 link	n.694_708dupGCAGCAGCAGCAGCA	non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR205HG	ENST00000366437.8 link	n.665_679dupGCAGCAGCAGCAGCA	non_coding_transcript_exon_variant	Exon 4 of 4	3
MIR205HG	ENST00000429156.7 link	n.776_790dupGCAGCAGCAGCAGCA	non_coding_transcript_exon_variant	Exon 5 of 5	3
MIR205HG	ENST00000431096.7 link	n.697_711dupGCAGCAGCAGCAGCA	non_coding_transcript_exon_variant	Exon 4 of 4	3

Frequencies

GnomAD3 genomes

AF:

0.000442

AC:

AN:

149472

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00134

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000532

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000216

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000296

Gnomad OTH

AF:

0.000486

GnomAD4 exome

AF:

0.0000532

AC:

AN:

1183538

Hom.:

Cov.:

AF XY:

0.0000461

AC XY:

AN XY:

585116

show subpopulations

African (AFR)

AF:

0.00131

AC:

AN:

25902

American (AMR)

AF:

0.000147

AC:

AN:

34060

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

16278

East Asian (EAS)

AF:

0.000183

AC:

AN:

16394

South Asian (SAS)

AF:

0.0000246

AC:

AN:

81278

European-Finnish (FIN)

AF:

0.00

AC:

AN:

30016

Middle Eastern (MID)

AF:

0.000240

AC:

AN:

4160

European-Non Finnish (NFE)

AF:

0.0000118

AC:

AN:

932548

Other (OTH)

AF:

0.000163

AC:

AN:

42902

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.530

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome 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

GnomAD4 genome

AF:

0.000441

AC:

AN:

149582

Hom.:

Cov.:

AF XY:

0.000356

AC XY:

AN XY:

72968

show subpopulations

African (AFR)

AF:

0.00134

AC:

AN:

40278

American (AMR)

AF:

0.000532

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:

0.000216

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:

0.0000296

AC:

AN:

67532

Other (OTH)

AF:

0.000481

AC:

AN:

2080

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

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:

0.000174

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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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