9-27510362-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_024761.5(MOB3B):c.-199+19193G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 152,040 control chromosomes in the GnomAD database, including 26,439 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 0.58 ( 26439 hom., cov: 33)
Consequence
MOB3B
NM_024761.5 intron
NM_024761.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.305
Publications
10 publications found
Genes affected
MOB3B (HGNC:23825): (MOB kinase activator 3B) The protein encoded by this gene shares similarity with the yeast Mob1 protein. Yeast Mob1 binds Mps1p, a protein kinase essential for spindle pole body duplication and mitotic checkpoint regulation. This gene is located on the opposite strand as the interferon kappa precursor (IFNK) gene. [provided by RefSeq, Jul 2008]
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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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.579 AC: 87971AN: 151922Hom.: 26442 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
87971
AN:
151922
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.579 AC: 87976AN: 152040Hom.: 26439 Cov.: 33 AF XY: 0.582 AC XY: 43231AN XY: 74326 show subpopulations
GnomAD4 genome
AF:
AC:
87976
AN:
152040
Hom.:
Cov.:
33
AF XY:
AC XY:
43231
AN XY:
74326
show subpopulations
African (AFR)
AF:
AC:
17340
AN:
41434
American (AMR)
AF:
AC:
9078
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
AC:
2486
AN:
3468
East Asian (EAS)
AF:
AC:
2920
AN:
5176
South Asian (SAS)
AF:
AC:
2569
AN:
4814
European-Finnish (FIN)
AF:
AC:
7793
AN:
10578
Middle Eastern (MID)
AF:
AC:
163
AN:
294
European-Non Finnish (NFE)
AF:
AC:
43791
AN:
67964
Other (OTH)
AF:
AC:
1247
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1858
3717
5575
7434
9292
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1686
AN:
3472
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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