chr9-27428667-A-T

Position:

• chr9-27428667-A-T

Variant summary

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

The NM_024761.5(MOB3B):​c.418+26466T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,162 control chromosomes in the GnomAD database, including 9,487 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 0.35 (9487 hom., cov: 33)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MOB3B	NM_024761.5	c.418+26466T>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.418+26466T>A		intron_variant		1	NM_024761.5	ENSP00000262244.5

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53024 AN: 152042 Hom.: 9490 Cov.: 33

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.348 AC: 53023 AN: 152162 Hom.: 9487 Cov.: 33 AF XY: 0.349 AC XY: 25988 AN XY: 74386

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.332

Alfa AF: 0.233 Hom.: 585

Bravo AF: 0.334

Asia WGS AF: 0.329 AC: 1142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.56
DANN	Benign	0.67

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: rs763372; hg19: chr9-27428665; COSMIC: COSV51777773;