9-27402963-A-G

Variant summary

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

The NM_024761.5(MOB3B):c.419-43727T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 152,088 control chromosomes in the GnomAD database, including 13,065 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 0.40 (13065 hom., cov: 33)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOB3B	NM_024761.5	c.419-43727T>C		intron_variant		ENST00000262244.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOB3B	ENST00000262244.6	c.419-43727T>C		intron_variant		1	NM_024761.5	P1
MOB3B	ENST00000603061.1	n.623+18129T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60480 AN: 151970 Hom.: 13032 Cov.: 33

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.398 AC: 60568 AN: 152088 Hom.: 13065 Cov.: 33 AF XY: 0.399 AC XY: 29668 AN XY: 74382

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.783

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.392

Alfa AF: 0.354 Hom.: 21694

Bravo AF: 0.414

Asia WGS AF: 0.674 AC: 2340 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.54
Dann	Benign	0.66

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: rs2150336; hg19: chr9-27402961;