rs3739530

Positions:

• chr9-27330516-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024761.5(MOB3B):​c.*71C>T variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.129 in 1,605,352 control chromosomes in the GnomAD database, including 15,351 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 0.17 (2850 hom., cov: 32)
  • Exomes 𝑓: 0.12 (12501 hom.)
• Consequence: MOB3B NM_024761.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.94

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MOB3B	NM_024761.5	c.*71C>T		3_prime_UTR_variant	4/4	ENST00000262244.6	NP_079037.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MOB3B	ENST00000262244.6	c.*71C>T		3_prime_UTR_variant	4/4	1	NM_024761.5	ENSP00000262244	P1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26566 AN: 151990 Hom.: 2844 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0957

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.165

GnomAD4 exome AF: 0.124 AC: 180379 AN: 1453244 Hom.: 12501 Cov.: 30 AF XY: 0.125 AC XY: 90583 AN XY: 722206

Gnomad4 AFR exome AF: 0.318

Gnomad4 AMR exome AF: 0.0765

Gnomad4 ASJ exome AF: 0.155

Gnomad4 EAS exome AF: 0.113

Gnomad4 SAS exome AF: 0.158

Gnomad4 FIN exome AF: 0.107

Gnomad4 NFE exome AF: 0.117

Gnomad4 OTH exome AF: 0.139

GnomAD4 genome AF: 0.175 AC: 26591 AN: 152108 Hom.: 2850 Cov.: 32 AF XY: 0.172 AC XY: 12789 AN XY: 74376

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.0961

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.163

Alfa AF: 0.137 Hom.: 2140

Bravo AF: 0.183

Asia WGS AF: 0.124 AC: 434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	10
DANN	Benign	0.78

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

Publications

LitVar

Other links and lift over

dbSNP: rs3739530; hg19: chr9-27330514; COSMIC: COSV51787546;