chr9-27502988-C-A

Variant names:

• chr9-27502988-C-A
• rs1977661
• NM_024761.5:c.-199+26567G>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.-199+26567G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,158 control chromosomes in the GnomAD database, including 1,412 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 (1412 hom., cov: 33)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552
• Publications: 13 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=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOB3B	NM_024761.5	c.-199+26567G>T		intron_variant	Intron 1 of 3	ENST00000262244.6	NP_079037.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOB3B	ENST00000262244.6	c.-199+26567G>T		intron_variant	Intron 1 of 3	1	NM_024761.5	ENSP00000262244.5

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19557 AN: 152040 Hom.: 1409 Cov.: 33

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.0815

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.0999

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.129 AC: 19569 AN: 152158 Hom.: 1412 Cov.: 33 AF XY: 0.131 AC XY: 9759 AN XY: 74384

African (AFR) AF: 0.137 AC: 5703 AN: 41484

American (AMR) AF: 0.176 AC: 2690 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 533 AN: 3466

East Asian (EAS) AF: 0.301 AC: 1556 AN: 5178

South Asian (SAS) AF: 0.197 AC: 950 AN: 4818

European-Finnish (FIN) AF: 0.0815 AC: 864 AN: 10604

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.0999 AC: 6795 AN: 68010

Other (OTH) AF: 0.142 AC: 299 AN: 2108

Alfa AF: 0.113 Hom.: 3473

Bravo AF: 0.136

Asia WGS AF: 0.191 AC: 663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.28
DANN	Benign	0.75
PhyloP100		-0.55
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: rs1977661; hg19: chr9-27502986; COSMIC: COSV51777982;