chr9-27495420-G-T

Position:

• chr9-27495420-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.-199+34135C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.884 in 152,096 control chromosomes in the GnomAD database, including 60,452 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 0.88 (60452 hom., cov: 30)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210

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 (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MOB3B	NM_024761.5	c.-199+34135C>A		intron_variant		ENST00000262244.6	NP_079037.3
MOB3B	XM_047423892.1	c.-199+2368C>A		intron_variant			XP_047279848.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MOB3B	ENST00000262244.6	c.-199+34135C>A		intron_variant		1	NM_024761.5	ENSP00000262244.5

Frequencies

GnomAD3 genomes AF: 0.884 AC: 134334 AN: 151978 Hom.: 60441 Cov.: 30

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.985

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.958

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.910

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

GnomAD4 genome AF: 0.884 AC: 134393 AN: 152096 Hom.: 60452 Cov.: 30 AF XY: 0.886 AC XY: 65878 AN XY: 74356

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.943

Gnomad4 ASJ AF: 0.985

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.904

Gnomad4 FIN AF: 0.958

Gnomad4 NFE AF: 0.956

Gnomad4 OTH AF: 0.905

Alfa AF: 0.942 Hom.: 49028

Bravo AF: 0.877

Asia WGS AF: 0.887 AC: 3085 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	1.6
DANN	Benign	0.80

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: rs2440622; hg19: chr9-27495418;