NM_024761.5:c.-198-22128G>A

Variant names:

• chr9-27477876-C-T
• rs1444533
• NM_024761.5:c.-198-22128G>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.-198-22128G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 152,054 control chromosomes in the GnomAD database, including 36,651 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 0.66 (36651 hom., cov: 32)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOB3B	NM_024761.5	c.-198-22128G>A		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.-198-22128G>A		intron_variant	Intron 1 of 3	1	NM_024761.5	ENSP00000262244.5

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100542 AN: 151936 Hom.: 36664 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.661 AC: 100548 AN: 152054 Hom.: 36651 Cov.: 32 AF XY: 0.662 AC XY: 49233 AN XY: 74332

African (AFR) AF: 0.339 AC: 14034 AN: 41434

American (AMR) AF: 0.702 AC: 10724 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2471 AN: 3468

East Asian (EAS) AF: 0.533 AC: 2748 AN: 5158

South Asian (SAS) AF: 0.672 AC: 3236 AN: 4814

European-Finnish (FIN) AF: 0.816 AC: 8628 AN: 10576

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56278 AN: 68008

Other (OTH) AF: 0.715 AC: 1507 AN: 2108

Alfa AF: 0.763 Hom.: 91208

Bravo AF: 0.636

Asia WGS AF: 0.572 AC: 1991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.21
PhyloP100		-0.26
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: rs1444533; hg19: chr9-27477874;