9-27361874-A-G

Variant names:

• chr9-27361874-A-G
• rs7849799
• NM_024761.5:c.419-2638T>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.419-2638T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,020 control chromosomes in the GnomAD database, including 4,074 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 (4074 hom., cov: 32)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOB3B	NM_024761.5	MANE Select	c.419-2638T>C		intron	N/A	NP_079037.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOB3B	ENST00000262244.6	TSL:1 MANE Select	c.419-2638T>C		intron	N/A	ENSP00000262244.5
	MOB3B	ENST00000603061.1	TSL:5	n.624-2638T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26911 AN: 151902 Hom.: 4059 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0603

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0596

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0889

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.177 AC: 26969 AN: 152020 Hom.: 4074 Cov.: 32 AF XY: 0.176 AC XY: 13112 AN XY: 74306

African (AFR) AF: 0.411 AC: 17021 AN: 41428

American (AMR) AF: 0.107 AC: 1631 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0603 AC: 209 AN: 3468

East Asian (EAS) AF: 0.000581 AC: 3 AN: 5166

South Asian (SAS) AF: 0.0588 AC: 283 AN: 4814

European-Finnish (FIN) AF: 0.128 AC: 1355 AN: 10564

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0889 AC: 6046 AN: 67982

Other (OTH) AF: 0.162 AC: 343 AN: 2114

Alfa AF: 0.126 Hom.: 4354

Bravo AF: 0.186

Asia WGS AF: 0.0470 AC: 164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.47
DANN	Benign	0.52
PhyloP100		-1.0
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: rs7849799; hg19: chr9-27361872;