rs4609281

Variant names:

• chr9-27514964-G-T
• rs4609281
• NM_024761.5:c.-199+14591C>A

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+14591C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 152,010 control chromosomes in the GnomAD database, including 32,368 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 0.64 (32368 hom., cov: 31)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326
• Publications: 4 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 (NFE) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024761.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOB3B	NM_024761.5	MANE Select	c.-199+14591C>A		intron	N/A	NP_079037.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOB3B	ENST00000262244.6	TSL:1 MANE Select	c.-199+14591C>A		intron	N/A	ENSP00000262244.5	Q86TA1
	MOB3B	ENST00000900190.1		c.-199+14591C>A		intron	N/A	ENSP00000570249.1
	MOB3B	ENST00000900189.1		c.-199+14220C>A		intron	N/A	ENSP00000570248.1

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97625 AN: 151892 Hom.: 32371 Cov.: 31

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.642 AC: 97641 AN: 152010 Hom.: 32368 Cov.: 31 AF XY: 0.644 AC XY: 47842 AN XY: 74288

African (AFR) AF: 0.474 AC: 19623 AN: 41430

American (AMR) AF: 0.644 AC: 9845 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 2626 AN: 3472

East Asian (EAS) AF: 0.700 AC: 3614 AN: 5160

South Asian (SAS) AF: 0.624 AC: 3002 AN: 4810

European-Finnish (FIN) AF: 0.783 AC: 8279 AN: 10576

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48467 AN: 67968

Other (OTH) AF: 0.655 AC: 1382 AN: 2110

Alfa AF: 0.682 Hom.: 10953

Bravo AF: 0.626

Asia WGS AF: 0.607 AC: 2114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.0
DANN	Benign	0.78
PhyloP100		0.33
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: rs4609281; hg19: chr9-27514962;