9-27481520-G-T

Position:

• chr9-27481520-G-T

Variant summary

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

The NM_024761.5(MOB3B):​c.-198-25772C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.27 (3225 hom., cov: 16)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOB3B	NM_024761.5	c.-198-25772C>A		intron_variant		ENST00000262244.6
MOB3B	XM_047423892.1	c.-199+16268C>A		intron_variant
MOB3B	XM_047423895.1	c.-199+3752C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOB3B	ENST00000262244.6	c.-198-25772C>A		intron_variant		1	NM_024761.5	P1

Frequencies

GnomAD3 genomes AF: 0.269 AC: 24479 AN: 91154 Hom.: 3228 Cov.: 16

Gnomad AFR AF: 0.0886

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.269 AC: 24483 AN: 91160 Hom.: 3225 Cov.: 16 AF XY: 0.258 AC XY: 10984 AN XY: 42510

Gnomad4 AFR AF: 0.0888

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.296

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.58

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: rs13295103; hg19: chr9-27481518; COSMIC: COSV51781270;