Variant rs903603 details in Genebe, Genetics Data Aggregator

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.18

Variant links:

Genes affected

LOC124902107 (HGNC:):

LOC124902107 links:

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]

MOB3B links:

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

EMICERI links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	Protein	UniProt
LOC124902107	XM_047424279.1 linkuse as main transcript	c.570G>A	p.Leu190=	synonymous_variant	2/2		XP_047280235.1
MOB3B	NM_024761.5 linkuse as main transcript	c.-199+237C>T		intron_variant		ENST00000262244.6	NP_079037.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MOB3B	ENST00000262244.6 linkuse as main transcript	c.-199+237C>T		intron_variant		1	NM_024761.5	ENSP00000262244	P1
EMICERI	ENST00000649931.1 linkuse as main transcript	n.234G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.398

AC:

60468

AN:

151970

Hom.:

14219

Cov.:

show subpopulations

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.:

AF XY:

0.403

AC XY:

29930

AN XY:

74336

show subpopulations

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

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over