9-27489253-A-G

Variant names:

• chr9-27489253-A-G
• rs868856
• NM_024761.5:c.-198-33505T>C

Variant summary

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

The NM_024761.5(MOB3B):​c.-198-33505T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 152,074 control chromosomes in the GnomAD database, including 31,968 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 (31968 hom., cov: 33)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 20 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 (NFE) allele frequency at 95% confidence interval = 0.709 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOB3B	NM_024761.5	MANE Select	c.-198-33505T>C		intron	N/A	NP_079037.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOB3B	ENST00000262244.6	TSL:1 MANE Select	c.-198-33505T>C		intron	N/A	ENSP00000262244.5

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96868 AN: 151956 Hom.: 31971 Cov.: 33

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.637 AC: 96883 AN: 152074 Hom.: 31968 Cov.: 33 AF XY: 0.638 AC XY: 47430 AN XY: 74342

African (AFR) AF: 0.461 AC: 19083 AN: 41438

American (AMR) AF: 0.633 AC: 9664 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2688 AN: 3472

East Asian (EAS) AF: 0.662 AC: 3420 AN: 5168

South Asian (SAS) AF: 0.631 AC: 3036 AN: 4814

European-Finnish (FIN) AF: 0.778 AC: 8245 AN: 10604

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

European-Non Finnish (NFE) AF: 0.714 AC: 48547 AN: 67988

Other (OTH) AF: 0.662 AC: 1395 AN: 2108

Alfa AF: 0.686 Hom.: 134458

Bravo AF: 0.619

Asia WGS AF: 0.601 AC: 2091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	9.5
DANN	Benign	0.75
PhyloP100		1.1
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: rs868856; hg19: chr9-27489251;