Variant 3-184711345-ATCCTCCTCCTCC-ATCCTCCTCCTCCTCC details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_022149.5(MAGEF1):c.474_476dupGGA(p.Glu158dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 1,567,356 control chromosomes in the GnomAD database, including 376,188 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.64 ( 31948 hom., cov: 0)

Exomes 𝑓: 0.69 ( 344240 hom. )

Consequence

MAGEF1
NM_022149.5 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.156

Variant links:

Genes affected

MAGEF1 (HGNC:29639): (MAGE family member F1) This intronless gene encodes a member of the MAGE superfamily. It is ubiquitously expressed in normal tissues and in tumor cells. This gene includes a microsatellite repeat in the coding region. [provided by RefSeq, Jul 2008]

MAGEF1 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 (NFE) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGEF1	NM_022149.5 linkuse as main transcript	c.474_476dupGGA	p.Glu158dup	disruptive_inframe_insertion	1/1	ENST00000317897.5	NP_071432.2	Q9HAY2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAGEF1	ENST00000317897.5 linkuse as main transcript	c.474_476dupGGA	p.Glu158dup	disruptive_inframe_insertion	1/1	6	NM_022149.5	ENSP00000315064.3		Q9HAY2

Frequencies

GnomAD3 genomes

AF:

0.641

AC:

96399

AN:

150310

Hom.:

31925

Cov.:

show subpopulations

Gnomad AFR

AF:

0.533

Gnomad AMI

AF:

0.544

Gnomad AMR

AF:

0.531

Gnomad ASJ

AF:

0.635

Gnomad EAS

AF:

0.388

Gnomad SAS

AF:

0.590

Gnomad FIN

AF:

0.706

Gnomad MID

AF:

0.679

Gnomad NFE

AF:

0.745

Gnomad OTH

AF:

0.665

GnomAD3 exomes

AF:

0.607

AC:

147082

AN:

242436

Hom.:

45698

AF XY:

0.618

AC XY:

81186

AN XY:

131400

show subpopulations

Gnomad AFR exome

AF:

0.516

Gnomad AMR exome

AF:

0.394

Gnomad ASJ exome

AF:

0.621

Gnomad EAS exome

AF:

0.382

Gnomad SAS exome

AF:

0.562

Gnomad FIN exome

AF:

0.669

Gnomad NFE exome

AF:

0.720

Gnomad OTH exome

AF:

0.653

GnomAD4 exome

AF:

0.694

AC:

983230

AN:

1416926

Hom.:

344240

Cov.:

AF XY:

0.692

AC XY:

488290

AN XY:

705654

show subpopulations

Gnomad4 AFR exome

AF:

0.518

Gnomad4 AMR exome

AF:

0.416

Gnomad4 ASJ exome

AF:

0.631

Gnomad4 EAS exome

AF:

0.351

Gnomad4 SAS exome

AF:

0.573

Gnomad4 FIN exome

AF:

0.689

Gnomad4 NFE exome

AF:

0.736

Gnomad4 OTH exome

AF:

0.674

GnomAD4 genome

AF:

0.641

AC:

96466

AN:

150430

Hom.:

31948

Cov.:

AF XY:

0.635

AC XY:

46674

AN XY:

73452

show subpopulations

Gnomad4 AFR

AF:

0.534

Gnomad4 AMR

AF:

0.530

Gnomad4 ASJ

AF:

0.635

Gnomad4 EAS

AF:

0.388

Gnomad4 SAS

AF:

0.590

Gnomad4 FIN

AF:

0.706

Gnomad4 NFE

AF:

0.745

Gnomad4 OTH

AF:

0.663

EpiCase

AF:

0.727

EpiControl

AF:

0.723

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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