Genetic Variant ENST00000366437.8:n.671_679delGCAGCAGCA (chr1-209432291-TAGCAGCAGC-T) – 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.671_679delGCAGCAGCA 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 0.000727 in 1,333,090 control chromosomes in the GnomAD database, including 3 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0021 ( 2 hom., cov: 0)

Exomes 𝑓: 0.00055 ( 1 hom. )

Consequence

MIR205HG
ENST00000366437.8 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.825

Publications

10 publications found

Variant links:

COSMIC-nc: COSV63532449

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 GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR205HG	NR_145433.1 link	n.617_625delGCAGCAGCA	non_coding_transcript_exon_variant	Exon 3 of 3
MIR205HG	NR_145434.1 link	n.752_760delGCAGCAGCA	non_coding_transcript_exon_variant	Exon 5 of 5
MIR205HG	NR_145435.1 link	n.700_708delGCAGCAGCA	non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR205HG	ENST00000366437.8 link	n.671_679delGCAGCAGCA	non_coding_transcript_exon_variant	Exon 4 of 4	3
MIR205HG	ENST00000429156.7 link	n.782_790delGCAGCAGCA	non_coding_transcript_exon_variant	Exon 5 of 5	3
MIR205HG	ENST00000431096.7 link	n.703_711delGCAGCAGCA	non_coding_transcript_exon_variant	Exon 4 of 4	3

Frequencies

GnomAD3 genomes

AF:

0.00214

AC:

320

AN:

149468

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00627

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00113

Gnomad ASJ

AF:

0.000290

Gnomad EAS

AF:

0.00258

Gnomad SAS

AF:

0.000863

Gnomad FIN

AF:

0.0000968

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000474

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000548

AC:

648

AN:

1183512

Hom.:

AF XY:

0.000545

AC XY:

319

AN XY:

585112

show subpopulations

African (AFR)

AF:

0.00676

AC:

175

AN:

25904

American (AMR)

AF:

0.000851

AC:

AN:

34060

Ashkenazi Jewish (ASJ)

AF:

0.0000614

AC:

AN:

16278

East Asian (EAS)

AF:

0.00219

AC:

AN:

16402

South Asian (SAS)

AF:

0.000984

AC:

AN:

81278

European-Finnish (FIN)

AF:

0.000133

AC:

AN:

30014

Middle Eastern (MID)

AF:

0.00144

AC:

AN:

4160

European-Non Finnish (NFE)

AF:

0.000290

AC:

270

AN:

932514

Other (OTH)

AF:

0.00110

AC:

AN:

42902

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

111

148

185

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.00215

AC:

321

AN:

149578

Hom.:

Cov.:

AF XY:

0.00207

AC XY:

151

AN XY:

72966

show subpopulations

African (AFR)

AF:

0.00628

AC:

253

AN:

40276

American (AMR)

AF:

0.00113

AC:

AN:

15046

Ashkenazi Jewish (ASJ)

AF:

0.000290

AC:

AN:

3454

East Asian (EAS)

AF:

0.00258

AC:

AN:

5034

South Asian (SAS)

AF:

0.000864

AC:

AN:

4630

European-Finnish (FIN)

AF:

0.0000968

AC:

AN:

10334

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.000474

AC:

AN:

67532

Other (OTH)

AF:

0.00

AC:

AN:

2080

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome 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

Alfa

AF:

0.00

Hom.:

2701

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.82

Mutation Taster

=97/3

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