rs2589054

chr9-27443804-A-Gchr9-27443804-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.418+11329T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,012 control chromosomes in the GnomAD database, including 12,242 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 0.39 (12242 hom., cov: 32)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.469

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOB3B	NM_024761.5	c.418+11329T>C		intron_variant		ENST00000262244.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOB3B	ENST00000262244.6	c.418+11329T>C		intron_variant		1	NM_024761.5	P1

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59348 AN: 151894 Hom.: 12217 Cov.: 32

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.391 AC: 59423 AN: 152012 Hom.: 12242 Cov.: 32 AF XY: 0.387 AC XY: 28761 AN XY: 74290

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.371

Alfa AF: 0.342 Hom.: 18299

Bravo AF: 0.392

Asia WGS AF: 0.332 AC: 1153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	4.7
Dann	Benign	0.66

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: rs2589054; hg19: chr9-27443802;