rs7046653

Positions:

• chr9-27490969-A-G
• chr9-27490969-A-T

Variant summary

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

The NM_024761.5(MOB3B):​c.-198-35221T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 147,204 control chromosomes in the GnomAD database, including 31,678 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 0.65 (31678 hom., cov: 29)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOB3B	NM_024761.5	c.-198-35221T>C		intron_variant		ENST00000262244.6
MOB3B	XM_047423892.1	c.-199+6819T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOB3B	ENST00000262244.6	c.-198-35221T>C		intron_variant		1	NM_024761.5	P1

Frequencies

GnomAD3 genomes AF: 0.653 AC: 96116 AN: 147096 Hom.: 31680 Cov.: 29

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.653 AC: 96133 AN: 147204 Hom.: 31678 Cov.: 29 AF XY: 0.656 AC XY: 47020 AN XY: 71660

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.785

Gnomad4 EAS AF: 0.681

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.795

Gnomad4 NFE AF: 0.727

Gnomad4 OTH AF: 0.680

Alfa AF: 0.699 Hom.: 80708

Bravo AF: 0.617

Asia WGS AF: 0.594 AC: 2065 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.61
DANN	Benign	0.64

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: rs7046653; hg19: chr9-27490967;