NM_024761.5:c.-199+10380G>A

Variant names:

• chr9-27519175-C-T
• rs11792285
• NM_024761.5:c.-199+10380G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024761.5(MOB3B):​c.-199+10380G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,026 control chromosomes in the GnomAD database, including 6,939 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 0.28 (6939 hom., cov: 31)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOB3B	NM_024761.5	c.-199+10380G>A		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.-199+10380G>A		intron_variant	Intron 1 of 3	1	NM_024761.5	ENSP00000262244.5

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42287 AN: 151908 Hom.: 6942 Cov.: 31

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.278 AC: 42282 AN: 152026 Hom.: 6939 Cov.: 31 AF XY: 0.275 AC XY: 20425 AN XY: 74300

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.282

Alfa AF: 0.344 Hom.: 12392

Bravo AF: 0.267

Asia WGS AF: 0.210 AC: 732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.13
DANN	Benign	0.61

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

Publications

LitVar

Other links and lift over

dbSNP: rs11792285; hg19: chr9-27519173; COSMIC: COSV51788713;