chr9-27445106-A-G

Variant names:

• chr9-27445106-A-G
• rs10812596
• NM_024761.5:c.418+10027T>C

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+10027T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,082 control chromosomes in the GnomAD database, including 6,816 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 0.29 (6816 hom., cov: 32)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024761.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOB3B	NM_024761.5	MANE Select	c.418+10027T>C		intron	N/A	NP_079037.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOB3B	ENST00000262244.6	TSL:1 MANE Select	c.418+10027T>C		intron	N/A	ENSP00000262244.5	Q86TA1
	MOB3B	ENST00000900190.1		c.418+10027T>C		intron	N/A	ENSP00000570249.1
	MOB3B	ENST00000900189.1		c.418+10027T>C		intron	N/A	ENSP00000570248.1

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44310 AN: 151964 Hom.: 6806 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.292 AC: 44351 AN: 152082 Hom.: 6816 Cov.: 32 AF XY: 0.295 AC XY: 21909 AN XY: 74330

African (AFR) AF: 0.217 AC: 8994 AN: 41480

American (AMR) AF: 0.359 AC: 5491 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1113 AN: 3470

East Asian (EAS) AF: 0.544 AC: 2809 AN: 5166

South Asian (SAS) AF: 0.436 AC: 2097 AN: 4812

European-Finnish (FIN) AF: 0.250 AC: 2645 AN: 10564

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20212 AN: 67994

Other (OTH) AF: 0.312 AC: 658 AN: 2110

Alfa AF: 0.292 Hom.: 5182

Bravo AF: 0.297

Asia WGS AF: 0.468 AC: 1626 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.4
DANN	Benign	0.71
PhyloP100		-0.53
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: rs10812596; hg19: chr9-27445104;