Genetic Variant ENST00000366437.8:n.674_679delGCAGCA (chr1-209432291-TAGCAGC-T) – 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.674_679delGCAGCA variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000156 in 1,333,096 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00028 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00014 ( 0 hom. )

Consequence

MIR205HG
ENST00000366437.8 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.799

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: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR205HG	NR_145433.1 link	n.620_625delGCAGCA	non_coding_transcript_exon_variant	Exon 3 of 3
MIR205HG	NR_145434.1 link	n.755_760delGCAGCA	non_coding_transcript_exon_variant	Exon 5 of 5
MIR205HG	NR_145435.1 link	n.703_708delGCAGCA	non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR205HG	ENST00000366437.8 link	n.674_679delGCAGCA	non_coding_transcript_exon_variant	Exon 4 of 4	3
MIR205HG	ENST00000429156.7 link	n.785_790delGCAGCA	non_coding_transcript_exon_variant	Exon 5 of 5	3
MIR205HG	ENST00000431096.7 link	n.706_711delGCAGCA	non_coding_transcript_exon_variant	Exon 4 of 4	3

Frequencies

GnomAD3 genomes

AF:

0.000261

AC:

AN:

149466

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000747

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000431

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000740

Gnomad OTH

AF:

0.000972

GnomAD4 exome

AF:

0.000140

AC:

166

AN:

1183520

Hom.:

AF XY:

0.000138

AC XY:

AN XY:

585108

show subpopulations

African (AFR)

AF:

0.000927

AC:

AN:

25902

American (AMR)

AF:

0.000117

AC:

AN:

34060

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

16278

East Asian (EAS)

AF:

0.00177

AC:

AN:

16402

South Asian (SAS)

AF:

0.000148

AC:

AN:

81278

European-Finnish (FIN)

AF:

0.00

AC:

AN:

30014

Middle Eastern (MID)

AF:

0.000481

AC:

AN:

4160

European-Non Finnish (NFE)

AF:

0.0000794

AC:

AN:

932524

Other (OTH)

AF:

0.000489

AC:

AN:

42902

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.466

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:

0.000281

AC:

AN:

149576

Hom.:

Cov.:

AF XY:

0.000260

AC XY:

AN XY:

72964

show subpopulations

African (AFR)

AF:

0.000819

AC:

AN:

40272

American (AMR)

AF:

0.00

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:

0.000432

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:

0.0000740

AC:

AN:

67532

Other (OTH)

AF:

0.000962

AC:

AN:

2080

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

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

0.80

Mutation Taster

=95/5

polymorphism

(source)

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