9-27451484-C-T

Variant names:

• chr9-27451484-C-T
• rs4879507
• NM_024761.5:c.418+3649G>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.418+3649G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,128 control chromosomes in the GnomAD database, including 3,028 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 0.19 (3028 hom., cov: 32)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 0 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]

ENSG00000300243 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 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.418+3649G>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.418+3649G>A		intron	N/A	ENSP00000262244.5
	MOB3B	ENST00000900190.1		c.418+3649G>A		intron	N/A	ENSP00000570249.1
	MOB3B	ENST00000900189.1		c.418+3649G>A		intron	N/A	ENSP00000570248.1

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28972 AN: 152008 Hom.: 3028 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.0338

Gnomad SAS AF: 0.0660

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.191 AC: 28994 AN: 152128 Hom.: 3028 Cov.: 32 AF XY: 0.188 AC XY: 13952 AN XY: 74372

African (AFR) AF: 0.230 AC: 9537 AN: 41496

American (AMR) AF: 0.153 AC: 2330 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1160 AN: 3470

East Asian (EAS) AF: 0.0335 AC: 174 AN: 5190

South Asian (SAS) AF: 0.0657 AC: 317 AN: 4828

European-Finnish (FIN) AF: 0.200 AC: 2117 AN: 10578

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12644 AN: 67984

Other (OTH) AF: 0.196 AC: 412 AN: 2102

Alfa AF: 0.185 Hom.: 10449

Bravo AF: 0.189

Asia WGS AF: 0.0610 AC: 213 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.019
DANN	Benign	0.66
PhyloP100		-1.9
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: rs4879507; hg19: chr9-27451482;