rs10967964

chr9-27495922-C-A

Variant summary

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

The NM_024761.5(MOB3B):c.-199+33633G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0965 in 152,200 control chromosomes in the GnomAD database, including 859 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 0.096 (859 hom., cov: 32)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOB3B	NM_024761.5	c.-199+33633G>T		intron_variant		ENST00000262244.6
MOB3B	XM_047423892.1	c.-199+1866G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOB3B	ENST00000262244.6	c.-199+33633G>T		intron_variant		1	NM_024761.5	P1
	ENST00000657557.1	n.1472G>T		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.0966 AC: 14688 AN: 152082 Hom.: 860 Cov.: 32

Gnomad AFR AF: 0.0259

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0949

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0965 AC: 14680 AN: 152200 Hom.: 859 Cov.: 32 AF XY: 0.100 AC XY: 7441 AN XY: 74386

Gnomad4 AFR AF: 0.0258

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0949

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.0999

Alfa AF: 0.113 Hom.: 860

Bravo AF: 0.0892

Asia WGS AF: 0.112 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.6
Dann	Benign	0.59

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: rs10967964; hg19: chr9-27495920; COSMIC: COSV51777962;