9-27430234-C-T

Variant names:

• chr9-27430234-C-T
• rs1161680
• NM_024761.5:c.418+24899G>A

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+24899G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 152,056 control chromosomes in the GnomAD database, including 26,172 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 0.58 (26172 hom., cov: 32)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOB3B	NM_024761.5	c.418+24899G>A		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+24899G>A		intron_variant	Intron 2 of 3	1	NM_024761.5	ENSP00000262244.5

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88220 AN: 151938 Hom.: 26160 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.580 AC: 88260 AN: 152056 Hom.: 26172 Cov.: 32 AF XY: 0.576 AC XY: 42848 AN XY: 74338

African (AFR) AF: 0.639 AC: 26489 AN: 41480

American (AMR) AF: 0.449 AC: 6860 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2101 AN: 3470

East Asian (EAS) AF: 0.353 AC: 1825 AN: 5166

South Asian (SAS) AF: 0.375 AC: 1809 AN: 4824

European-Finnish (FIN) AF: 0.657 AC: 6956 AN: 10582

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.591 AC: 40186 AN: 67952

Other (OTH) AF: 0.562 AC: 1182 AN: 2102

Alfa AF: 0.577 Hom.: 111138

Bravo AF: 0.565

Asia WGS AF: 0.379 AC: 1319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.61
DANN	Benign	0.60
PhyloP100		-0.24
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: rs1161680; hg19: chr9-27430232;