dbSNP rs7949144: MIR194-2HG:n.2280C>G (chr11-64890927-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000413053.2(MIR194-2HG):n.2280C>G 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 0.0394 in 243,176 control chromosomes in the GnomAD database, including 300 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.040 ( 173 hom., cov: 31)

Exomes 𝑓: 0.039 ( 127 hom. )

Consequence

MIR194-2HG
ENST00000413053.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.75

Publications

3 publications found

Variant links:

Genes affected

MIR194-2HG (HGNC:51946): (MIR194-2 host gene)

MIR194-2HG links:

MIR192 (HGNC:31562): (microRNA 192) 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]

MIR192 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR194-2HG	NR_133638.1 link	n.2280C>G	non_coding_transcript_exon_variant	Exon 2 of 2
MIR194-2HG	NR_133639.1 link	n.437+1502C>G	intron_variant	Intron 2 of 2
MIR194-2HG	NR_133640.1 link	n.277-1587C>G	intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR194-2HG	ENST00000413053.2 link	n.2280C>G	non_coding_transcript_exon_variant	Exon 2 of 2	2
MIR194-2HG	ENST00000710929.1 link	n.391-1587C>G	intron_variant	Intron 3 of 3
MIR194-2HG	ENST00000710930.1 link	n.551+1502C>G	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0400

AC:

6082

AN:

152132

Hom.:

173

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0104

Gnomad AMI

AF:

0.0516

Gnomad AMR

AF:

0.0378

Gnomad ASJ

AF:

0.0942

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0126

Gnomad FIN

AF:

0.0948

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.0513

Gnomad OTH

AF:

0.0469

GnomAD4 exome

AF:

0.0386

AC:

3507

AN:

90926

Hom.:

127

Cov.:

AF XY:

0.0354

AC XY:

1791

AN XY:

50602

show subpopulations

African (AFR)

AF:

0.00783

AC:

AN:

1150

American (AMR)

AF:

0.0293

AC:

113

AN:

3860

Ashkenazi Jewish (ASJ)

AF:

0.0962

AC:

167

AN:

1736

East Asian (EAS)

AF:

0.00

AC:

AN:

1250

South Asian (SAS)

AF:

0.0144

AC:

313

AN:

21762

European-Finnish (FIN)

AF:

0.0826

AC:

447

AN:

5412

Middle Eastern (MID)

AF:

0.0765

AC:

AN:

340

European-Non Finnish (NFE)

AF:

0.0434

AC:

2214

AN:

50984

Other (OTH)

AF:

0.0492

AC:

218

AN:

4432

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

150

301

451

602

752

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:

0.0399

AC:

6081

AN:

152250

Hom.:

173

Cov.:

AF XY:

0.0413

AC XY:

3071

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.0104

AC:

434

AN:

41540

American (AMR)

AF:

0.0377

AC:

577

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0942

AC:

327

AN:

3472

East Asian (EAS)

AF:

0.000193

AC:

AN:

5168

South Asian (SAS)

AF:

0.0124

AC:

AN:

4834

European-Finnish (FIN)

AF:

0.0948

AC:

1005

AN:

10604

Middle Eastern (MID)

AF:

0.156

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0512

AC:

3486

AN:

68020

Other (OTH)

AF:

0.0464

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

308

615

923

1230

1538

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

222

296

370

<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:

0.0479

Hom.:

Bravo

AF:

0.0351

Asia WGS

AF:

0.00895

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

9.0

(source)

DANN

Benign

0.69

PhyloP100

1.8

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