rs895023

chr9-27483961-G-Achr9-27483961-G-Cchr9-27483961-G-T

Variant summary

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

The NM_024761.5(MOB3B):c.-198-28213C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.91 in 152,232 control chromosomes in the GnomAD database, including 63,559 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 0.91 (63559 hom., cov: 32)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOB3B	NM_024761.5	c.-198-28213C>T		intron_variant		ENST00000262244.6
MOB3B	XM_047423892.1	c.-199+13827C>T		intron_variant
MOB3B	XM_047423895.1	c.-199+1311C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOB3B	ENST00000262244.6	c.-198-28213C>T		intron_variant		1	NM_024761.5	P1

Frequencies

GnomAD3 genomes AF: 0.910 AC: 138488 AN: 152114 Hom.: 63541 Cov.: 32

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.953

Gnomad ASJ AF: 0.985

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.958

Gnomad MID AF: 0.920

Gnomad NFE AF: 0.958

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.910 AC: 138559 AN: 152232 Hom.: 63559 Cov.: 32 AF XY: 0.912 AC XY: 67907 AN XY: 74440

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.953

Gnomad4 ASJ AF: 0.985

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.913

Gnomad4 FIN AF: 0.958

Gnomad4 NFE AF: 0.958

Gnomad4 OTH AF: 0.923

Alfa AF: 0.952 Hom.: 107001

Bravo AF: 0.907

Asia WGS AF: 0.904 AC: 3144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.89
Dann	Benign	0.30

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: rs895023; hg19: chr9-27483959;