dbSNP rs58463981: MIR200CHG:n.1811C>T (chr12-6963834-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000732834.1(MIR200CHG):n.1811C>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 0.0355 in 249,182 control chromosomes in the GnomAD database, including 865 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 0.056 ( 838 hom., cov: 32)

Exomes 𝑓: 0.0038 ( 27 hom. )

Consequence

MIR200CHG
ENST00000732834.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.123

Publications

0 publications found

Variant links:

Genes affected

MIR200CHG (HGNC:53161): (MIR200C and MIR141 host gene)

MIR200CHG links:

MIR200C (HGNC:31580): (microRNA 200c) 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]

MIR200C 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=-0.78).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR200CHG	NR_135032.1 link	n.105-367C>T	intron_variant	Intron 1 of 1
MIR200C	NR_029779.1 link	n.*68C>T	downstream_gene_variant
MIR200C	unassigned_transcript_1981	n.*110C>T	downstream_gene_variant
MIR200C	unassigned_transcript_1982	n.*70C>T	downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR200CHG	ENST00000732834.1 link	n.1811C>T	non_coding_transcript_exon_variant	Exon 1 of 1
MIR200CHG	ENST00000537269.3 link	n.224-367C>T	intron_variant	Intron 1 of 1	2
MIR200CHG	ENST00000732835.1 link	n.120-367C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0555

AC:

8445

AN:

152102

Hom.:

834

Cov.:

show subpopulations

Gnomad AFR

AF:

0.192

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0194

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0119

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000823

Gnomad OTH

AF:

0.0416

GnomAD4 exome

AF:

0.00376

AC:

365

AN:

96962

Hom.:

AF XY:

0.00297

AC XY:

158

AN XY:

53204

show subpopulations

African (AFR)

AF:

0.192

AC:

251

AN:

1306

American (AMR)

AF:

0.00989

AC:

AN:

4246

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1682

East Asian (EAS)

AF:

0.00468

AC:

AN:

1924

South Asian (SAS)

AF:

0.000149

AC:

AN:

20088

European-Finnish (FIN)

AF:

0.00

AC:

AN:

18916

Middle Eastern (MID)

AF:

0.00778

AC:

AN:

1414

European-Non Finnish (NFE)

AF:

0.000390

AC:

AN:

43584

Other (OTH)

AF:

0.00842

AC:

AN:

3802

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome 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

GnomAD4 genome

AF:

0.0557

AC:

8478

AN:

152220

Hom.:

838

Cov.:

AF XY:

0.0549

AC XY:

4083

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.192

AC:

7977

AN:

41490

American (AMR)

AF:

0.0193

AC:

295

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.0120

AC:

AN:

5182

South Asian (SAS)

AF:

0.000207

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000823

AC:

AN:

68010

Other (OTH)

AF:

0.0412

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

340

680

1021

1361

1701

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

168

252

336

420

<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:

0.0442

Hom.:

Bravo

AF:

0.0631

Asia WGS

AF:

0.0190

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

4.8

(source)

DANN

Benign

0.89

PhyloP100

-0.12

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