rs2589054

Variant names:

• chr9-27443804-A-G
• rs2589054
• NM_024761.5:c.418+11329T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-27443804-A-G
• chr9-27443804-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MOB3B	NM_024761.5	c.418+11329T>C		intron_variant	Intron 2 of 3	ENST00000262244.6	NP_079037.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOB3B	ENST00000262244.6	c.418+11329T>C		intron_variant	Intron 2 of 3	1	NM_024761.5	ENSP00000262244.5

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

African (AFR) AF: 0.532 AC: 22051 AN: 41462

American (AMR) AF: 0.300 AC: 4593 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1570 AN: 3470

East Asian (EAS) AF: 0.320 AC: 1653 AN: 5158

South Asian (SAS) AF: 0.304 AC: 1464 AN: 4818

European-Finnish (FIN) AF: 0.367 AC: 3871 AN: 10562

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23063 AN: 67938

Other (OTH) AF: 0.371 AC: 786 AN: 2116

Alfa AF: 0.350 Hom.: 40046

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
PhyloP100		0.47
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2589054; hg19: chr9-27443802;