rs2120718

Positions:

• chr9-27438413-C-T

Variant summary

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

The NM_024761.5(MOB3B):​c.418+16720G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,148 control chromosomes in the GnomAD database, including 2,867 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 0.18 (2867 hom., cov: 32)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35

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 = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MOB3B	NM_024761.5	c.418+16720G>A		intron_variant		ENST00000262244.6	NP_079037.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MOB3B	ENST00000262244.6	c.418+16720G>A		intron_variant		1	NM_024761.5	ENSP00000262244.5

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27963 AN: 152030 Hom.: 2867 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0599

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.184 AC: 27972 AN: 152148 Hom.: 2867 Cov.: 32 AF XY: 0.181 AC XY: 13481 AN XY: 74390

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0599

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.199

Alfa AF: 0.211 Hom.: 2570

Bravo AF: 0.177

Asia WGS AF: 0.0390 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.095
DANN	Benign	0.55

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: rs2120718; hg19: chr9-27438411;