rs4879515

Variant names:

• chr9-27482237-C-T
• rs4879515
• NM_024761.5:c.-198-26489G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_024761.5(MOB3B):​c.-198-26489G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 151,888 control chromosomes in the GnomAD database, including 19,132 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 0.50 (19132 hom., cov: 31)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200
• Publications: 11 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOB3B	NM_024761.5	c.-198-26489G>A		intron_variant	Intron 1 of 3	ENST00000262244.6	NP_079037.3
MOB3B	XM_047423892.1	c.-199+15551G>A		intron_variant	Intron 1 of 3		XP_047279848.1
MOB3B	XM_047423895.1	c.-199+3035G>A		intron_variant	Intron 1 of 3		XP_047279851.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOB3B	ENST00000262244.6	c.-198-26489G>A		intron_variant	Intron 1 of 3	1	NM_024761.5	ENSP00000262244.5

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75522 AN: 151770 Hom.: 19119 Cov.: 31

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.498 AC: 75576 AN: 151888 Hom.: 19132 Cov.: 31 AF XY: 0.502 AC XY: 37271 AN XY: 74236

African (AFR) AF: 0.524 AC: 21701 AN: 41378

American (AMR) AF: 0.574 AC: 8769 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1550 AN: 3464

East Asian (EAS) AF: 0.656 AC: 3387 AN: 5166

South Asian (SAS) AF: 0.540 AC: 2602 AN: 4816

European-Finnish (FIN) AF: 0.446 AC: 4688 AN: 10518

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.458 AC: 31090 AN: 67950

Other (OTH) AF: 0.516 AC: 1090 AN: 2112

Alfa AF: 0.472 Hom.: 15559

Bravo AF: 0.512

Asia WGS AF: 0.552 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	14
DANN	Benign	0.78
PhyloP100		0.020
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: rs4879515; hg19: chr9-27482235;