Genetic Variant MAGEF1:p.Glu158dup (chr3-184711345-A-ATCC) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP3BA1

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

Publications

12 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -9 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_022149.5

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 rank	MANE	Protein	UniProt
MAGEF1	NM_022149.5 link	c.474_476dupGGA	p.Glu158dup	disruptive_inframe_insertion	Exon 1 of 1	ENST00000317897.5	NP_071432.2	Q9HAY2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAGEF1	ENST00000317897.5 link	c.474_476dupGGA	p.Glu158dup	disruptive_inframe_insertion	Exon 1 of 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

GnomAD2 exomes

AF:

0.607

AC:

147082

AN:

242436

AF XY:

0.618

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 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

African (AFR)

AF:

0.518

AC:

17080

AN:

33004

American (AMR)

AF:

0.416

AC:

18439

AN:

44320

Ashkenazi Jewish (ASJ)

AF:

0.631

AC:

16145

AN:

25600

East Asian (EAS)

AF:

0.351

AC:

13890

AN:

39548

South Asian (SAS)

AF:

0.573

AC:

48481

AN:

84682

European-Finnish (FIN)

AF:

0.689

AC:

35080

AN:

50932

Middle Eastern (MID)

AF:

0.668

AC:

3795

AN:

5684

European-Non Finnish (NFE)

AF:

0.736

AC:

790572

AN:

1074208

Other (OTH)

AF:

0.674

AC:

39748

AN:

58948

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

18779

37557

56336

75114

93893

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19220

38440

57660

76880

96100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.641

AC:

96466

AN:

150430

Hom.:

31948

Cov.:

AF XY:

0.635

AC XY:

46674

AN XY:

73452

show subpopulations

African (AFR)

AF:

0.534

AC:

21852

AN:

40952

American (AMR)

AF:

0.530

AC:

8037

AN:

15150

Ashkenazi Jewish (ASJ)

AF:

0.635

AC:

2191

AN:

3452

East Asian (EAS)

AF:

0.388

AC:

1978

AN:

5094

South Asian (SAS)

AF:

0.590

AC:

2793

AN:

4734

European-Finnish (FIN)

AF:

0.706

AC:

7284

AN:

10324

Middle Eastern (MID)

AF:

0.688

AC:

198

AN:

288

European-Non Finnish (NFE)

AF:

0.745

AC:

50253

AN:

67438

Other (OTH)

AF:

0.663

AC:

1387

AN:

2092

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1581

3162

4744

6325

7906

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

768

1536

2304

3072

3840

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.614

Hom.:

3040

EpiCase

AF:

0.727

EpiControl

AF:

0.723

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.16

Mutation Taster

=82/18

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over