rs1316679

Variant names:

• chr9-27452242-G-A
• rs1316679
• NM_024761.5:c.418+2891C>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+2891C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,090 control chromosomes in the GnomAD database, including 1,290 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 0.13 (1290 hom., cov: 32)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOB3B	NM_024761.5	c.418+2891C>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+2891C>T		intron_variant	Intron 2 of 3	1	NM_024761.5	ENSP00000262244.5
ENSG00000300243	ENST00000770344.1	n.149-6014G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19145 AN: 151972 Hom.: 1284 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.0648

Gnomad AMR AF: 0.0871

Gnomad ASJ AF: 0.0737

Gnomad EAS AF: 0.0297

Gnomad SAS AF: 0.0918

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.126 AC: 19171 AN: 152090 Hom.: 1290 Cov.: 32 AF XY: 0.125 AC XY: 9313 AN XY: 74330

African (AFR) AF: 0.173 AC: 7171 AN: 41488

American (AMR) AF: 0.0871 AC: 1330 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0737 AC: 256 AN: 3472

East Asian (EAS) AF: 0.0295 AC: 153 AN: 5178

South Asian (SAS) AF: 0.0921 AC: 443 AN: 4812

European-Finnish (FIN) AF: 0.147 AC: 1556 AN: 10570

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7921 AN: 67976

Other (OTH) AF: 0.117 AC: 248 AN: 2112

Alfa AF: 0.115 Hom.: 677

Bravo AF: 0.122

Asia WGS AF: 0.0670 AC: 237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.36
DANN	Benign	0.80
PhyloP100		-0.065
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: rs1316679; hg19: chr9-27452240; COSMIC: COSV51788159;