rs700795

chr9-27520510-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024761.5(MOB3B):c.-199+9045T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,084 control chromosomes in the GnomAD database, including 4,628 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 0.24 (4628 hom., cov: 33)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.636

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOB3B	NM_024761.5	c.-199+9045T>C		intron_variant		ENST00000262244.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOB3B	ENST00000262244.6	c.-199+9045T>C		intron_variant		1	NM_024761.5	P1

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36901 AN: 151966 Hom.: 4614 Cov.: 33

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.243 AC: 36945 AN: 152084 Hom.: 4628 Cov.: 33 AF XY: 0.244 AC XY: 18123 AN XY: 74346

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.250

Alfa AF: 0.244 Hom.: 1266

Bravo AF: 0.253

Asia WGS AF: 0.284 AC: 986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
Cadd	Benign	7.6
Dann	Benign	0.86

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

Publications

LitVar

Other links and lift over

dbSNP: rs700795; hg19: chr9-27520508;