GeneBe

chr1-1163440-TC-T

Variant names:

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

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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MIR200BHGXR_007065348.1 linkn.383-186delC intron_variant Intron 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.879
AC:
133322
AN:
151608
Hom.:
59121
Cov.:
0
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.:
0
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
0
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
0
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 v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
-0.41

Splicing

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

Publications

Other links and lift over

dbSNP: rs5772039; hg19: chr1-1098820; API