9-27481520-G-T

Variant names:

• chr9-27481520-G-T
• rs13295103
• NM_024761.5:c.-198-25772C>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.-198-25772C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.27 (3225 hom., cov: 16)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 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.-198-25772C>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.-198-25772C>A		intron	N/A	ENSP00000262244.5	Q86TA1
	MOB3B	ENST00000900190.1		c.-198-25772C>A		intron	N/A	ENSP00000570249.1
	MOB3B	ENST00000900189.1		c.-198-25772C>A		intron	N/A	ENSP00000570248.1

Frequencies

GnomAD3 genomes AF: 0.269 AC: 24479 AN: 91154 Hom.: 3228 Cov.: 16

Gnomad AFR AF: 0.0886

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.269 AC: 24483 AN: 91160 Hom.: 3225 Cov.: 16 AF XY: 0.258 AC XY: 10984 AN XY: 42510

African (AFR) AF: 0.0888 AC: 2499 AN: 28142

American (AMR) AF: 0.222 AC: 1688 AN: 7616

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 748 AN: 2040

East Asian (EAS) AF: 0.210 AC: 436 AN: 2080

South Asian (SAS) AF: 0.226 AC: 584 AN: 2580

European-Finnish (FIN) AF: 0.216 AC: 717 AN: 3324

Middle Eastern (MID) AF: 0.321 AC: 59 AN: 184

European-Non Finnish (NFE) AF: 0.396 AC: 17170 AN: 43314

Other (OTH) AF: 0.296 AC: 357 AN: 1208

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.58
PhyloP100		0.0
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13295103; hg19: chr9-27481518; COSMIC: COSV51781270;