chr9-27372055-A-C

Variant names:

• chr9-27372055-A-C
• rs10121765
• NM_024761.5:c.419-12819T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024761.5(MOB3B):​c.419-12819T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,036 control chromosomes in the GnomAD database, including 25,301 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 0.57 (25301 hom., cov: 32)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377
• Publications: 4 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOB3B	NM_024761.5	MANE Select	c.419-12819T>G		intron	N/A	NP_079037.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOB3B	ENST00000262244.6	TSL:1 MANE Select	c.419-12819T>G		intron	N/A	ENSP00000262244.5
	MOB3B	ENST00000603061.1	TSL:5	n.624-12819T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86540 AN: 151918 Hom.: 25261 Cov.: 32

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.570 AC: 86634 AN: 152036 Hom.: 25301 Cov.: 32 AF XY: 0.571 AC XY: 42392 AN XY: 74296

African (AFR) AF: 0.689 AC: 28578 AN: 41450

American (AMR) AF: 0.515 AC: 7868 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1274 AN: 3472

East Asian (EAS) AF: 0.384 AC: 1983 AN: 5168

South Asian (SAS) AF: 0.559 AC: 2696 AN: 4826

European-Finnish (FIN) AF: 0.591 AC: 6236 AN: 10548

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.534 AC: 36331 AN: 67980

Other (OTH) AF: 0.545 AC: 1149 AN: 2110

Alfa AF: 0.534 Hom.: 13985

Bravo AF: 0.564

Asia WGS AF: 0.503 AC: 1751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.72
PhyloP100		-0.38
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: rs10121765; hg19: chr9-27372053; COSMIC: COSV51787732;