rs903603

chr9-27529318-G-Achr9-27529318-G-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The XM_047424279.1(LOC124902107):c.570G>A(p.Leu190=) variant causes a synonymous 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: LOC124902107 XM_047424279.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

Genes affected

LOC124902107 (HGNC:):

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]

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

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902107	XM_047424279.1	c.570G>A	p.Leu190=	synonymous_variant	2/2
MOB3B	NM_024761.5	c.-199+237C>T		intron_variant		ENST00000262244.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOB3B	ENST00000262244.6	c.-199+237C>T		intron_variant		1	NM_024761.5	P1
EMICERI	ENST00000649931.1	n.234G>A		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.417

Alfa AF: 0.476 Hom.: 23754

Bravo AF: 0.383

Asia WGS AF: 0.442 AC: 1536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	17
Dann	Benign	0.92

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

Publications

LitVar

Other links and lift over

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