rs1031154

Variant names:

• chr9-27498802-A-C
• rs1031154
• NM_024761.5:c.-199+30753T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602
• Publications: 2 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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MOB3B	NM_024761.5	c.-199+30753T>G		intron_variant	Intron 1 of 3	ENST00000262244.6	NP_079037.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOB3B	ENST00000262244.6	c.-199+30753T>G		intron_variant	Intron 1 of 3	1	NM_024761.5	ENSP00000262244.5

Frequencies

GnomAD3 genomes AF: 0.886 AC: 134803 AN: 152086 Hom.: 60774 Cov.: 32

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

African (AFR) AF: 0.702 AC: 29093 AN: 41470

American (AMR) AF: 0.944 AC: 14444 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.985 AC: 3419 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5146 AN: 5176

South Asian (SAS) AF: 0.913 AC: 4406 AN: 4824

European-Finnish (FIN) AF: 0.963 AC: 10229 AN: 10618

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.957 AC: 65068 AN: 68026

Other (OTH) AF: 0.907 AC: 1917 AN: 2114

Alfa AF: 0.925 Hom.: 40477

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
PhyloP100		-0.60
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1031154; hg19: chr9-27498800;