rs1110264

Variant names:

• chr9-27385004-G-A
• rs1110264
• NM_024761.5:c.419-25768C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-27385004-G-A
• chr9-27385004-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.419-25768C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,020 control chromosomes in the GnomAD database, including 8,413 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 0.31 (8413 hom., cov: 32)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOB3B	NM_024761.5	c.419-25768C>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.419-25768C>T		intron_variant	Intron 2 of 3	1	NM_024761.5	ENSP00000262244.5
MOB3B	ENST00000603061.1	n.624-25768C>T		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47026 AN: 151902 Hom.: 8399 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.310 AC: 47078 AN: 152020 Hom.: 8413 Cov.: 32 AF XY: 0.315 AC XY: 23409 AN XY: 74308

African (AFR) AF: 0.318 AC: 13177 AN: 41436

American (AMR) AF: 0.368 AC: 5619 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1212 AN: 3472

East Asian (EAS) AF: 0.787 AC: 4061 AN: 5162

South Asian (SAS) AF: 0.576 AC: 2767 AN: 4806

European-Finnish (FIN) AF: 0.186 AC: 1970 AN: 10580

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17279 AN: 67972

Other (OTH) AF: 0.332 AC: 702 AN: 2114

Alfa AF: 0.286 Hom.: 4420

Bravo AF: 0.323

Asia WGS AF: 0.662 AC: 2298 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.74
PhyloP100		-0.45
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs1110264; hg19: chr9-27385002;