dbSNP rs72563729: MIR200B:n.80G>A (chr1-1167183-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBS1BS2

The ENST00000384997.3(MIR200B):n.80G>A 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 0.0141 in 531,854 control chromosomes in the GnomAD database, including 94 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 0.012 ( 20 hom., cov: 33)

Exomes 𝑓: 0.015 ( 74 hom. )

Consequence

MIR200B
ENST00000384997.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.511

Publications

10 publications found

Variant links:

Genes affected

MIR200B (HGNC:31579): (microRNA 200b) 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]

MIR200B links:

MIR200BHG (HGNC:58145):

MIR200BHG links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0118 (1801/152240) while in subpopulation NFE AF = 0.0198 (1349/67974). AF 95% confidence interval is 0.019. There are 20 homozygotes in GnomAd4. There are 839 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 20 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR200B	NR_029639.1 link	n.80G>A	non_coding_transcript_exon_variant	Exon 1 of 1
MIR200BHG	XR_007065348.1 link	n.3931G>A	non_coding_transcript_exon_variant	Exon 2 of 2
MIR200B	unassigned_transcript_7	n.*38G>A	downstream_gene_variant
MIR200B	unassigned_transcript_8	n.*2G>A	downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR200B	ENST00000384997.3 link	n.80G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.0118

AC:

1802

AN:

152122

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00292

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00661

Gnomad ASJ

AF:

0.00951

Gnomad EAS

AF:

0.000384

Gnomad SAS

AF:

0.0178

Gnomad FIN

AF:

0.00773

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0198

Gnomad OTH

AF:

0.00861

GnomAD2 exomes

AF:

0.0127

AC:

3103

AN:

243388

AF XY:

0.0130

show subpopulations

Gnomad AFR exome

AF:

0.00240

Gnomad AMR exome

AF:

0.00633

Gnomad ASJ exome

AF:

0.00970

Gnomad EAS exome

AF:

0.0000553

Gnomad FIN exome

AF:

0.00986

Gnomad NFE exome

AF:

0.0182

Gnomad OTH exome

AF:

0.0172

GnomAD4 exome

AF:

0.0151

AC:

5715

AN:

379614

Hom.:

Cov.:

AF XY:

0.0156

AC XY:

3378

AN XY:

216124

show subpopulations

African (AFR)

AF:

0.00257

AC:

AN:

10506

American (AMR)

AF:

0.00673

AC:

243

AN:

36122

Ashkenazi Jewish (ASJ)

AF:

0.0102

AC:

118

AN:

11620

East Asian (EAS)

AF:

0.00

AC:

AN:

13114

South Asian (SAS)

AF:

0.0167

AC:

1111

AN:

66372

European-Finnish (FIN)

AF:

0.0100

AC:

311

AN:

31104

Middle Eastern (MID)

AF:

0.0166

AC:

AN:

2834

European-Non Finnish (NFE)

AF:

0.0190

AC:

3635

AN:

191334

Other (OTH)

AF:

0.0134

AC:

223

AN:

16608

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

279

557

836

1114

1393

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:

0.0118

AC:

1801

AN:

152240

Hom.:

Cov.:

AF XY:

0.0113

AC XY:

839

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.00291

AC:

121

AN:

41548

American (AMR)

AF:

0.00654

AC:

100

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.00951

AC:

AN:

3470

East Asian (EAS)

AF:

0.000385

AC:

AN:

5190

South Asian (SAS)

AF:

0.0180

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.00773

AC:

AN:

10614

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0198

AC:

1349

AN:

67974

Other (OTH)

AF:

0.00852

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

191

286

382

477

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

<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:

0.0145

Hom.:

Bravo

AF:

0.0103

Asia WGS

AF:

0.00722

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

(source)

DANN

Benign

0.75

PhyloP100

0.51

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