chr9-27529318-G-A

Variant names:

• chr9-27529318-G-A
• rs903603
• NM_024761.5:c.-199+237C>T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_024761.5(MOB3B):​c.-199+237C>T 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 14,216 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 (14216 hom., cov: 33)
• Consequence: MOB3B NM_024761.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 21 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]

LOC124902107 (HGNC:):

EMICERI (HGNC:53656): (EQTN MOB3B IFNK C9orf72 enhancer RNA I)

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024761.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOB3B	NM_024761.5	MANE Select	c.-199+237C>T		intron	N/A	NP_079037.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOB3B	ENST00000262244.6	TSL:1 MANE Select	c.-199+237C>T		intron	N/A	ENSP00000262244.5
	EMICERI	ENST00000649931.1		n.234G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60468 AN: 151970 Hom.: 14219 Cov.: 33

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.398 AC: 60456 AN: 152088 Hom.: 14216 Cov.: 33 AF XY: 0.403 AC XY: 29930 AN XY: 74336

African (AFR) AF: 0.136 AC: 5652 AN: 41530

American (AMR) AF: 0.471 AC: 7200 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2189 AN: 3472

East Asian (EAS) AF: 0.595 AC: 3052 AN: 5130

South Asian (SAS) AF: 0.463 AC: 2233 AN: 4822

European-Finnish (FIN) AF: 0.507 AC: 5353 AN: 10554

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33336 AN: 67968

Other (OTH) AF: 0.417 AC: 879 AN: 2110

Alfa AF: 0.467 Hom.: 28663

Bravo AF: 0.383

Asia WGS AF: 0.442 AC: 1536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	17
DANN	Benign	0.92
PhyloP100		1.2
PromoterAI		0.094	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.35		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.35		Position offset: 2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs903603; hg19: chr9-27529316; COSMIC: COSV51778002; COSMIC: COSV51778002;