chr9-27498802-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024761.5(MOB3B):​c.-199+30753T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.886 in 152,206 control chromosomes in the GnomAD database, including 60,785 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 0.89 ( 60785 hom., cov: 32)

Consequence

MOB3B
NM_024761.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.602
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MOB3BNM_024761.5 linkuse as main transcriptc.-199+30753T>G intron_variant ENST00000262244.6 NP_079037.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MOB3BENST00000262244.6 linkuse as main transcriptc.-199+30753T>G intron_variant 1 NM_024761.5 ENSP00000262244 P1

Frequencies

GnomAD3 genomes
AF:
0.886
AC:
134803
AN:
152086
Hom.:
60774
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.702
Gnomad AMI
AF:
0.957
Gnomad AMR
AF:
0.944
Gnomad ASJ
AF:
0.985
Gnomad EAS
AF:
0.994
Gnomad SAS
AF:
0.913
Gnomad FIN
AF:
0.963
Gnomad MID
AF:
0.905
Gnomad NFE
AF:
0.957
Gnomad OTH
AF:
0.912
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.886
AC:
134861
AN:
152206
Hom.:
60785
Cov.:
32
AF XY:
0.889
AC XY:
66170
AN XY:
74430
show subpopulations
Gnomad4 AFR
AF:
0.702
Gnomad4 AMR
AF:
0.944
Gnomad4 ASJ
AF:
0.985
Gnomad4 EAS
AF:
0.994
Gnomad4 SAS
AF:
0.913
Gnomad4 FIN
AF:
0.963
Gnomad4 NFE
AF:
0.957
Gnomad4 OTH
AF:
0.907
Alfa
AF:
0.928
Hom.:
24514
Bravo
AF:
0.879
Asia WGS
AF:
0.895
AC:
3112
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
4.4
DANN
Benign
0.71

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1031154; hg19: chr9-27498800; API