rs1822723

Positions:

• chr9-27478054-C-T

Variant summary

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

The ENST00000262244.6(MOB3B):​c.-198-22306G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 151,950 control chromosomes in the GnomAD database, including 5,191 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 0.25 (5191 hom., cov: 33)
• Consequence: MOB3B ENST00000262244.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.822

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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MOB3B	NM_024761.5	c.-198-22306G>A		intron_variant		ENST00000262244.6	NP_079037.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MOB3B	ENST00000262244.6	c.-198-22306G>A		intron_variant		1	NM_024761.5	ENSP00000262244	P1

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37355 AN: 151832 Hom.: 5195 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.246 AC: 37366 AN: 151950 Hom.: 5191 Cov.: 33 AF XY: 0.251 AC XY: 18625 AN XY: 74266

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.260

Alfa AF: 0.273 Hom.: 9490

Bravo AF: 0.243

Asia WGS AF: 0.352 AC: 1224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.24
DANN	Benign	0.43

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: rs1822723; hg19: chr9-27478052; COSMIC: COSV51777909;