Genetic Variant MIR200BHG:n.383-186delC (chr1-1163440-TC-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The XR_007065348.1(MIR200BHG):n.383-186delC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.88 ( 59169 hom., cov: 0)

Consequence

MIR200BHG
XR_007065348.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.406

Publications

0 publications found

Variant links:

Genes affected

MIR200BHG (HGNC:58145):

MIR200BHG links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Variant Effect in Transcripts

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes

AF:

0.879

AC:

133322

AN:

151608

Hom.:

59121

Cov.:

show subpopulations

Gnomad AFR

AF:

0.817

Gnomad AMI

AF:

0.990

Gnomad AMR

AF:

0.898

Gnomad ASJ

AF:

0.910

Gnomad EAS

AF:

0.567

Gnomad SAS

AF:

0.882

Gnomad FIN

AF:

0.900

Gnomad MID

AF:

0.949

Gnomad NFE

AF:

0.930

Gnomad OTH

AF:

0.876

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.879

AC:

133426

AN:

151724

Hom.:

59169

Cov.:

AF XY:

0.877

AC XY:

65046

AN XY:

74156

show subpopulations

African (AFR)

AF:

0.817

AC:

33791

AN:

41362

American (AMR)

AF:

0.898

AC:

13711

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.910

AC:

3155

AN:

3466

East Asian (EAS)

AF:

0.568

AC:

2902

AN:

5110

South Asian (SAS)

AF:

0.882

AC:

4246

AN:

4814

European-Finnish (FIN)

AF:

0.900

AC:

9492

AN:

10550

Middle Eastern (MID)

AF:

0.945

AC:

276

AN:

292

European-Non Finnish (NFE)

AF:

0.930

AC:

63107

AN:

67854

Other (OTH)

AF:

0.877

AC:

1843

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

777

1554

2331

3108

3885

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

888

1776

2664

3552

4440

<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:

0.880

Hom.:

1870

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.41

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over