rs2225389

Variant names:

• chr9-27409266-T-G
• rs2225389
• NM_024761.5:c.418+45867A>C

Variant summary

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

The NM_024761.5(MOB3B):​c.418+45867A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.077 in 152,272 control chromosomes in the GnomAD database, including 529 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 0.077 (529 hom., cov: 32)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 8 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOB3B	NM_024761.5	c.418+45867A>C		intron_variant	Intron 2 of 3	ENST00000262244.6	NP_079037.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOB3B	ENST00000262244.6	c.418+45867A>C		intron_variant	Intron 2 of 3	1	NM_024761.5	ENSP00000262244.5
MOB3B	ENST00000603061.1	n.623+11826A>C		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.0769 AC: 11706 AN: 152154 Hom.: 526 Cov.: 32

Gnomad AFR AF: 0.0378

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0785

Gnomad ASJ AF: 0.0692

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0940

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0933

Gnomad OTH AF: 0.0597

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0770 AC: 11720 AN: 152272 Hom.: 529 Cov.: 32 AF XY: 0.0782 AC XY: 5820 AN XY: 74462

African (AFR) AF: 0.0379 AC: 1577 AN: 41562

American (AMR) AF: 0.0783 AC: 1198 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0692 AC: 240 AN: 3470

East Asian (EAS) AF: 0.115 AC: 597 AN: 5170

South Asian (SAS) AF: 0.124 AC: 599 AN: 4830

European-Finnish (FIN) AF: 0.0940 AC: 997 AN: 10606

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0933 AC: 6345 AN: 68016

Other (OTH) AF: 0.0647 AC: 137 AN: 2116

Alfa AF: 0.0883 Hom.: 542

Bravo AF: 0.0718

Asia WGS AF: 0.121 AC: 421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.026
DANN	Benign	0.71
PhyloP100		-1.3
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: rs2225389; hg19: chr9-27409264;