9-27498802-A-C

Position:

• chr9-27498802-A-C

Variant summary

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

The NM_024761.5(MOB3B):​c.-199+30753T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.886 in 152,206 control chromosomes in the GnomAD database, including 60,785 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 0.89 (60785 hom., cov: 32)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MOB3B	NM_024761.5	c.-199+30753T>G		intron_variant		ENST00000262244.6	NP_079037.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MOB3B	ENST00000262244.6	c.-199+30753T>G		intron_variant		1	NM_024761.5	ENSP00000262244	P1

Frequencies

GnomAD3 genomes AF: 0.886 AC: 134803 AN: 152086 Hom.: 60774 Cov.: 32

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.944

Gnomad ASJ AF: 0.985

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.963

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.957

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.886 AC: 134861 AN: 152206 Hom.: 60785 Cov.: 32 AF XY: 0.889 AC XY: 66170 AN XY: 74430

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.944

Gnomad4 ASJ AF: 0.985

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.913

Gnomad4 FIN AF: 0.963

Gnomad4 NFE AF: 0.957

Gnomad4 OTH AF: 0.907

Alfa AF: 0.928 Hom.: 24514

Bravo AF: 0.879

Asia WGS AF: 0.895 AC: 3112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.4
DANN	Benign	0.71

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: rs1031154; hg19: chr9-27498800;