Genetic Variant MAGEF1:p.Glu157_Glu158dup (chr3-184711345-A-ATCCTCC) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP3BP6_ModerateBS1BS2

The NM_022149.5(MAGEF1):c.471_476dupGGAGGA(p.Glu157_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 0.00226 in 1,567,536 control chromosomes in the GnomAD database, including 36 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0085 ( 12 hom., cov: 0)

Exomes 𝑓: 0.0016 ( 24 hom. )

Consequence

MAGEF1
NM_022149.5 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

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 -11 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_022149.5

BP6

Variant 3-184711345-A-ATCCTCC is Benign according to our data. Variant chr3-184711345-A-ATCCTCC is described in ClinVar as Benign. ClinVar VariationId is 403067.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00855 (1287/150552) while in subpopulation AFR AF = 0.0277 (1135/40980). AF 95% confidence interval is 0.0264. There are 12 homozygotes in GnomAd4. There are 609 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 12 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022149.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGEF1	NM_022149.5	MANE Select	c.471_476dupGGAGGA	p.Glu157_Glu158dup	disruptive_inframe_insertion	Exon 1 of 1	NP_071432.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGEF1	ENST00000317897.5	TSL:6 MANE Select	c.471_476dupGGAGGA	p.Glu157_Glu158dup	disruptive_inframe_insertion	Exon 1 of 1	ENSP00000315064.3	Q9HAY2

Frequencies

GnomAD3 genomes

AF:

0.00853

AC:

1283

AN:

150432

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0277

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00284

Gnomad ASJ

AF:

0.00984

Gnomad EAS

AF:

0.000392

Gnomad SAS

AF:

0.000632

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00325

Gnomad NFE

AF:

0.000800

Gnomad OTH

AF:

0.00674

GnomAD2 exomes

AF:

0.00301

AC:

730

AN:

242436

AF XY:

0.00243

show subpopulations

Gnomad AFR exome

AF:

0.0304

Gnomad AMR exome

AF:

0.00152

Gnomad ASJ exome

AF:

0.0117

Gnomad EAS exome

AF:

0.000441

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000603

Gnomad OTH exome

AF:

0.00204

GnomAD4 exome

AF:

0.00159

AC:

2257

AN:

1416984

Hom.:

Cov.:

AF XY:

0.00147

AC XY:

1035

AN XY:

705666

show subpopulations

African (AFR)

AF:

0.0332

AC:

1097

AN:

33008

American (AMR)

AF:

0.00180

AC:

AN:

44324

Ashkenazi Jewish (ASJ)

AF:

0.0121

AC:

311

AN:

25602

East Asian (EAS)

AF:

0.000253

AC:

AN:

39552

South Asian (SAS)

AF:

0.000248

AC:

AN:

84684

European-Finnish (FIN)

AF:

0.0000196

AC:

AN:

50980

Middle Eastern (MID)

AF:

0.00246

AC:

AN:

5684

European-Non Finnish (NFE)

AF:

0.000510

AC:

548

AN:

1074198

Other (OTH)

AF:

0.00297

AC:

175

AN:

58952

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.464

Heterozygous variant carriers

140

280

419

559

699

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

108

162

216

270

<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:

0.00855

AC:

1287

AN:

150552

Hom.:

Cov.:

AF XY:

0.00828

AC XY:

609

AN XY:

73526

show subpopulations

African (AFR)

AF:

0.0277

AC:

1135

AN:

40980

American (AMR)

AF:

0.00284

AC:

AN:

15166

Ashkenazi Jewish (ASJ)

AF:

0.00984

AC:

AN:

3454

East Asian (EAS)

AF:

0.000392

AC:

AN:

5096

South Asian (SAS)

AF:

0.000633

AC:

AN:

4740

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10348

Middle Eastern (MID)

AF:

0.00347

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.000800

AC:

AN:

67476

Other (OTH)

AF:

0.00715

AC:

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

130

194

259

324

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.00323

Hom.:

3040

EpiCase

AF:

0.000709

EpiControl

AF:

0.000949

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.16

Mutation Taster

=82/18

polymorphism

(source)

Splicing

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

Publications

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3-184711345-ATCCTCCTCCTCC-ATCCTCCTCCTCCTCCTCC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over