Genetic Variant MIR205HG:n.677_679delGCA (chr1-209432291-TAGC-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1BS2

The ENST00000366437.8(MIR205HG):n.677_679delGCA 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 0.00339 in 1,329,502 control chromosomes in the GnomAD database, including 68 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.013 ( 42 hom., cov: 0)

Exomes 𝑓: 0.0021 ( 26 hom. )

Consequence

MIR205HG
ENST00000366437.8 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.749

Publications

10 publications found

Variant links:

COSMIC-nc: COSV63532607

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: Benign. The variant received -8 ACMG points.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0132 (1976/149556) while in subpopulation AFR AF = 0.0449 (1806/40258). AF 95% confidence interval is 0.0431. There are 42 homozygotes in GnomAd4. There are 937 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 42 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR205HG	NR_145433.1 link	n.623_625delGCA	non_coding_transcript_exon_variant	Exon 3 of 3
MIR205HG	NR_145434.1 link	n.758_760delGCA	non_coding_transcript_exon_variant	Exon 5 of 5
MIR205HG	NR_145435.1 link	n.706_708delGCA	non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR205HG	ENST00000366437.8 link	n.677_679delGCA	non_coding_transcript_exon_variant	Exon 4 of 4	3
MIR205HG	ENST00000429156.7 link	n.788_790delGCA	non_coding_transcript_exon_variant	Exon 5 of 5	3
MIR205HG	ENST00000431096.7 link	n.709_711delGCA	non_coding_transcript_exon_variant	Exon 4 of 4	3

Frequencies

GnomAD3 genomes

AF:

0.0132

AC:

1972

AN:

149446

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0449

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00459

Gnomad ASJ

AF:

0.00174

Gnomad EAS

AF:

0.000793

Gnomad SAS

AF:

0.00151

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00955

Gnomad NFE

AF:

0.000874

Gnomad OTH

AF:

0.0107

GnomAD2 exomes

AF:

0.00397

AC:

772

AN:

194576

AF XY:

0.00352

show subpopulations

Gnomad AFR exome

AF:

0.0410

Gnomad AMR exome

AF:

0.00244

Gnomad ASJ exome

AF:

0.00274

Gnomad EAS exome

AF:

0.00176

Gnomad FIN exome

AF:

0.000985

Gnomad NFE exome

AF:

0.00135

Gnomad OTH exome

AF:

0.00264

GnomAD4 exome

AF:

0.00214

AC:

2529

AN:

1179946

Hom.:

AF XY:

0.00211

AC XY:

1230

AN XY:

583424

show subpopulations

African (AFR)

AF:

0.0464

AC:

1193

AN:

25718

American (AMR)

AF:

0.00242

AC:

AN:

33942

Ashkenazi Jewish (ASJ)

AF:

0.00283

AC:

AN:

16238

East Asian (EAS)

AF:

0.00141

AC:

AN:

16336

South Asian (SAS)

AF:

0.00235

AC:

190

AN:

80886

European-Finnish (FIN)

AF:

0.000669

AC:

AN:

29898

Middle Eastern (MID)

AF:

0.00241

AC:

AN:

4144

European-Non Finnish (NFE)

AF:

0.000852

AC:

792

AN:

930016

Other (OTH)

AF:

0.00405

AC:

173

AN:

42768

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

127

253

380

506

633

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

132

198

264

330

<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:

0.0132

AC:

1976

AN:

149556

Hom.:

Cov.:

AF XY:

0.0128

AC XY:

937

AN XY:

72958

show subpopulations

African (AFR)

AF:

0.0449

AC:

1806

AN:

40258

American (AMR)

AF:

0.00459

AC:

AN:

15046

Ashkenazi Jewish (ASJ)

AF:

0.00174

AC:

AN:

3456

East Asian (EAS)

AF:

0.000795

AC:

AN:

5034

South Asian (SAS)

AF:

0.00151

AC:

AN:

4628

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10332

Middle Eastern (MID)

AF:

0.0103

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.000874

AC:

AN:

67530

Other (OTH)

AF:

0.0106

AC:

AN:

2080

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

166

250

333

416

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

110

<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:

0.00302

Hom.:

2701

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.75

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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