rs2069031

Variant names:

• chr9-27427259-G-A
• rs2069031
• NM_024761.5:c.418+27874C>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.418+27874C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,208 control chromosomes in the GnomAD database, including 2,071 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 0.15 (2071 hom., cov: 32)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276
• Publications: 1 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024761.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOB3B	NM_024761.5	MANE Select	c.418+27874C>T		intron	N/A	NP_079037.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOB3B	ENST00000262244.6	TSL:1 MANE Select	c.418+27874C>T		intron	N/A	ENSP00000262244.5
	MOB3B	ENST00000900190.1		c.418+27874C>T		intron	N/A	ENSP00000570249.1
	MOB3B	ENST00000900189.1		c.418+27874C>T		intron	N/A	ENSP00000570248.1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23255 AN: 152090 Hom.: 2072 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0557

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.153 AC: 23250 AN: 152208 Hom.: 2071 Cov.: 32 AF XY: 0.151 AC XY: 11227 AN XY: 74430

African (AFR) AF: 0.105 AC: 4360 AN: 41534

American (AMR) AF: 0.132 AC: 2023 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1143 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5178

South Asian (SAS) AF: 0.0558 AC: 269 AN: 4822

European-Finnish (FIN) AF: 0.199 AC: 2110 AN: 10592

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12675 AN: 67998

Other (OTH) AF: 0.174 AC: 368 AN: 2114

Alfa AF: 0.179 Hom.: 532

Bravo AF: 0.148

Asia WGS AF: 0.0320 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.6
DANN	Benign	0.55
PhyloP100		-0.28
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: rs2069031; hg19: chr9-27427257;