rs1058326

Variant names:

• chr9-27447091-G-A
• rs1058326
• NM_024761.5:c.418+8042C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-27447091-G-A
• chr9-27447091-G-C

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+8042C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 151,958 control chromosomes in the GnomAD database, including 11,543 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 0.38 (11543 hom., cov: 31)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 8 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]

ENSG00000300243 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOB3B	NM_024761.5	c.418+8042C>T		intron_variant	Intron 2 of 3	ENST00000262244.6	NP_079037.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOB3B	ENST00000262244.6	c.418+8042C>T		intron_variant	Intron 2 of 3	1	NM_024761.5	ENSP00000262244.5
ENSG00000300243	ENST00000770344.1	n.148+1460G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58290 AN: 151840 Hom.: 11543 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.384 AC: 58326 AN: 151958 Hom.: 11543 Cov.: 31 AF XY: 0.382 AC XY: 28361 AN XY: 74250

African (AFR) AF: 0.381 AC: 15791 AN: 41450

American (AMR) AF: 0.390 AC: 5955 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 939 AN: 3470

East Asian (EAS) AF: 0.174 AC: 902 AN: 5176

South Asian (SAS) AF: 0.282 AC: 1357 AN: 4808

European-Finnish (FIN) AF: 0.425 AC: 4478 AN: 10528

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27585 AN: 67946

Other (OTH) AF: 0.371 AC: 784 AN: 2114

Alfa AF: 0.386 Hom.: 23009

Bravo AF: 0.381

Asia WGS AF: 0.258 AC: 895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.65
PhyloP100		-0.27
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: rs1058326; hg19: chr9-27447089; COSMIC: COSV51777819;