rs774354

Variant summary

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

The NM_024761.5(MOB3B):​c.-199+13586T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,190 control chromosomes in the GnomAD database, including 6,617 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 0.29 ( 6617 hom., cov: 33)

Consequence

MOB3B
NM_024761.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.35
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 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+13586T>C 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+13586T>C intron_variant 1 NM_024761.5 ENSP00000262244 P1

Frequencies

GnomAD3 genomes
AF:
0.291
AC:
44320
AN:
152072
Hom.:
6597
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.324
Gnomad AMI
AF:
0.315
Gnomad AMR
AF:
0.323
Gnomad ASJ
AF:
0.237
Gnomad EAS
AF:
0.296
Gnomad SAS
AF:
0.320
Gnomad FIN
AF:
0.216
Gnomad MID
AF:
0.361
Gnomad NFE
AF:
0.276
Gnomad OTH
AF:
0.287
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.292
AC:
44379
AN:
152190
Hom.:
6617
Cov.:
33
AF XY:
0.292
AC XY:
21720
AN XY:
74430
show subpopulations
Gnomad4 AFR
AF:
0.325
Gnomad4 AMR
AF:
0.323
Gnomad4 ASJ
AF:
0.237
Gnomad4 EAS
AF:
0.296
Gnomad4 SAS
AF:
0.322
Gnomad4 FIN
AF:
0.216
Gnomad4 NFE
AF:
0.276
Gnomad4 OTH
AF:
0.285
Alfa
AF:
0.281
Hom.:
2623
Bravo
AF:
0.302
Asia WGS
AF:
0.321
AC:
1114
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
6.2
DANN
Benign
0.65

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: rs774354; hg19: chr9-27515967; API