rs765709

Variant names:

• chr9-27451962-A-C
• rs765709
• NM_024761.5:c.418+3171T>G

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+3171T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0817 in 152,302 control chromosomes in the GnomAD database, including 665 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 0.082 (665 hom., cov: 33)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.242
• Publications: 5 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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 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.418+3171T>G		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.418+3171T>G		intron	N/A	ENSP00000262244.5
	ENSG00000300243	ENST00000770344.1		n.149-6294A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0818 AC: 12448 AN: 152182 Hom.: 664 Cov.: 33

Gnomad AFR AF: 0.0216

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0678

Gnomad ASJ AF: 0.0662

Gnomad EAS AF: 0.0297

Gnomad SAS AF: 0.0908

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0812

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

GnomAD4 genome AF: 0.0817 AC: 12450 AN: 152302 Hom.: 665 Cov.: 33 AF XY: 0.0832 AC XY: 6198 AN XY: 74466

African (AFR) AF: 0.0216 AC: 896 AN: 41576

American (AMR) AF: 0.0678 AC: 1036 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0662 AC: 230 AN: 3472

East Asian (EAS) AF: 0.0297 AC: 154 AN: 5178

South Asian (SAS) AF: 0.0911 AC: 440 AN: 4830

European-Finnish (FIN) AF: 0.147 AC: 1559 AN: 10616

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7875 AN: 68018

Other (OTH) AF: 0.0808 AC: 171 AN: 2116

Alfa AF: 0.103 Hom.: 1509

Bravo AF: 0.0710

Asia WGS AF: 0.0540 AC: 192 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.3
DANN	Benign	0.66
PhyloP100		0.24
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: rs765709; hg19: chr9-27451960; COSMIC: COSV51788141;