chr9-27489253-A-G

Position:

• chr9-27489253-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_024761.5(MOB3B):​c.-198-33505T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 152,074 control chromosomes in the GnomAD database, including 31,968 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 0.64 (31968 hom., cov: 33)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOB3B	NM_024761.5	c.-198-33505T>C		intron_variant		ENST00000262244.6
MOB3B	XM_047423892.1	c.-199+8535T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOB3B	ENST00000262244.6	c.-198-33505T>C		intron_variant		1	NM_024761.5	P1

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96868 AN: 151956 Hom.: 31971 Cov.: 33

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.637 AC: 96883 AN: 152074 Hom.: 31968 Cov.: 33 AF XY: 0.638 AC XY: 47430 AN XY: 74342

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.662

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.662

Alfa AF: 0.698 Hom.: 59943

Bravo AF: 0.619

Asia WGS AF: 0.601 AC: 2091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	9.5
DANN	Benign	0.75

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: rs868856; hg19: chr9-27489251;