11-64891364-G-A

Variant names:

Variant summary

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

The ENST00000413053.2(MIR194-2HG):n.1843C>T 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 0.00725 in 521,136 control chromosomes in the GnomAD database, including 139 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 0.019 ( 106 hom., cov: 32)

Exomes 𝑓: 0.0025 ( 33 hom. )

Consequence

MIR194-2HG
ENST00000413053.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.758

Publications

10 publications found

Variant links:

Genes affected

MIR194-2 (HGNC:31565): (microRNA 194-2) 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]

MIR194-2 links:

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:

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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=-0.6).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0622 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413053.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
MIR194-2	NR_029829.1	n.76C>T	non_coding_transcript_exon	Exon 1 of 1
MIR194-2HG	NR_133638.1	n.1843C>T	non_coding_transcript_exon	Exon 2 of 2
MIR194-2HG	NR_133639.1	n.437+1065C>T	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
MIR194-2	ENST00000384864.1	TSL:6	n.76C>T	non_coding_transcript_exon	Exon 1 of 1
MIR194-2HG	ENST00000413053.2	TSL:2	n.1843C>T	non_coding_transcript_exon	Exon 2 of 2
MIR194-2HG	ENST00000710929.1		n.390+1226C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0187

AC:

2838

AN:

152014

Hom.:

106

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0643

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00779

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.000580

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000294

Gnomad OTH

AF:

0.0148

GnomAD2 exomes

AF:

0.00484

AC:

1090

AN:

225156

AF XY:

0.00353

show subpopulations

Gnomad AFR exome

AF:

0.0654

Gnomad AMR exome

AF:

0.00360

Gnomad ASJ exome

AF:

0.00265

Gnomad EAS exome

AF:

0.000469

Gnomad FIN exome

AF:

0.0000524

Gnomad NFE exome

AF:

0.000261

Gnomad OTH exome

AF:

0.00252

GnomAD4 exome

AF:

0.00254

AC:

936

AN:

369004

Hom.:

Cov.:

AF XY:

0.00187

AC XY:

393

AN XY:

209762

show subpopulations

African (AFR)

AF:

0.0662

AC:

684

AN:

10326

American (AMR)

AF:

0.00363

AC:

126

AN:

34682

Ashkenazi Jewish (ASJ)

AF:

0.00237

AC:

AN:

11376

East Asian (EAS)

AF:

0.000238

AC:

AN:

12594

South Asian (SAS)

AF:

0.0000619

AC:

AN:

64598

European-Finnish (FIN)

AF:

0.00

AC:

AN:

30668

Middle Eastern (MID)

AF:

0.00179

AC:

AN:

2796

European-Non Finnish (NFE)

AF:

0.000178

AC:

AN:

185876

Other (OTH)

AF:

0.00336

AC:

AN:

16088

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.453

Heterozygous variant carriers

128

170

213

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:

0.0187

AC:

2844

AN:

152132

Hom.:

106

Cov.:

AF XY:

0.0176

AC XY:

1311

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.0642

AC:

2665

AN:

41484

American (AMR)

AF:

0.00778

AC:

119

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.00173

AC:

AN:

3466

East Asian (EAS)

AF:

0.000581

AC:

AN:

5164

South Asian (SAS)

AF:

0.00

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10606

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000294

AC:

AN:

67982

Other (OTH)

AF:

0.0147

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

124

248

373

497

621

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

140

<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:

0.00610

Hom.:

Bravo

AF:

0.0209

Asia WGS

AF:

0.00173

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

6.4

(source)

DANN

Benign

0.88

PhyloP100

-0.76

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over