rs10511816

Variant names:

• chr9-27468463-C-A
• rs10511816
• NM_024761.5:c.-198-12715G>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.-198-12715G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,140 control chromosomes in the GnomAD database, including 8,273 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 0.30 (8273 hom., cov: 32)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 13 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOB3B	NM_024761.5	c.-198-12715G>T		intron_variant	Intron 1 of 3	ENST00000262244.6	NP_079037.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOB3B	ENST00000262244.6	c.-198-12715G>T		intron_variant	Intron 1 of 3	1	NM_024761.5	ENSP00000262244.5

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45202 AN: 152022 Hom.: 8281 Cov.: 32

Gnomad AFR AF: 0.0990

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.297 AC: 45184 AN: 152140 Hom.: 8273 Cov.: 32 AF XY: 0.298 AC XY: 22137 AN XY: 74340

African (AFR) AF: 0.0987 AC: 4102 AN: 41544

American (AMR) AF: 0.325 AC: 4969 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 958 AN: 3468

East Asian (EAS) AF: 0.109 AC: 565 AN: 5184

South Asian (SAS) AF: 0.220 AC: 1062 AN: 4822

European-Finnish (FIN) AF: 0.425 AC: 4484 AN: 10548

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.410 AC: 27870 AN: 67978

Other (OTH) AF: 0.327 AC: 690 AN: 2112

Alfa AF: 0.370 Hom.: 22832

Bravo AF: 0.281

Asia WGS AF: 0.181 AC: 629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.40
DANN	Benign	0.53
PhyloP100		-1.1
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: rs10511816; hg19: chr9-27468461;