Genetic Variant MAGEC1:p.Glu1058Glu (chrX-141908578-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_005462.5(MAGEC1):c.3174G>A(p.Glu1058Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 1,201,785 control chromosomes in the GnomAD database, including 10,033 homozygotes. There are 61,860 hemizygotes in GnomAD. 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 0.14 ( 858 hom., 4678 hem., cov: 23)

Exomes 𝑓: 0.16 ( 9175 hom. 57182 hem. )

Consequence

MAGEC1
NM_005462.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.291

Publications

7 publications found

Variant links:

Genes affected

MAGEC1 (HGNC:6812): (MAGE family member C1) This gene is a member of the melanoma antigen gene (MAGE) family. The proteins of this family are tumor-specific antigens that can be recognized by autologous cytolytic T lymphocytes. This protein contains a large number of unique short repetitive sequences in front of the MAGE-homologous sequence, and therefore is about 800 aa longer than the other MAGE proteins. [provided by RefSeq, Jul 2008]

MAGEC1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP7

Synonymous conserved (PhyloP=0.291 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAGEC1	NM_005462.5 link	c.3174G>A	p.Glu1058Glu	synonymous_variant	Exon 4 of 4	ENST00000285879.5	NP_005453.2	O60732-1
MAGEC1	XM_011531418.3 link	c.3174G>A	p.Glu1058Glu	synonymous_variant	Exon 4 of 4		XP_011529720.1	O60732-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAGEC1	ENST00000285879.5 link	c.3174G>A	p.Glu1058Glu	synonymous_variant	Exon 4 of 4	1	NM_005462.5	ENSP00000285879.4		O60732-1
MAGEC1	ENST00000406005.2 link	c.375G>A	p.Glu125Glu	synonymous_variant	Exon 4 of 4	1		ENSP00000385500.2		O60732-2

Frequencies

GnomAD3 genomes

AF:

0.144

AC:

15917

AN:

110857

Hom.:

860

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.168

Gnomad AMR

AF:

0.108

Gnomad ASJ

AF:

0.146

Gnomad EAS

AF:

0.128

Gnomad SAS

AF:

0.191

Gnomad FIN

AF:

0.165

Gnomad MID

AF:

0.0928

Gnomad NFE

AF:

0.164

Gnomad OTH

AF:

0.119

GnomAD2 exomes

AF:

0.148

AC:

25829

AN:

174142

AF XY:

0.153

show subpopulations

Gnomad AFR exome

AF:

0.120

Gnomad AMR exome

AF:

0.0869

Gnomad ASJ exome

AF:

0.145

Gnomad EAS exome

AF:

0.128

Gnomad FIN exome

AF:

0.172

Gnomad NFE exome

AF:

0.163

Gnomad OTH exome

AF:

0.146

GnomAD4 exome

AF:

0.158

AC:

171838

AN:

1090876

Hom.:

9175

Cov.:

AF XY:

0.160

AC XY:

57182

AN XY:

357648

show subpopulations

African (AFR)

AF:

0.119

AC:

3129

AN:

26219

American (AMR)

AF:

0.0880

AC:

3052

AN:

34687

Ashkenazi Jewish (ASJ)

AF:

0.146

AC:

2750

AN:

18828

East Asian (EAS)

AF:

0.129

AC:

3889

AN:

30130

South Asian (SAS)

AF:

0.195

AC:

10285

AN:

52850

European-Finnish (FIN)

AF:

0.177

AC:

7125

AN:

40253

Middle Eastern (MID)

AF:

0.0986

AC:

403

AN:

4088

European-Non Finnish (NFE)

AF:

0.160

AC:

134219

AN:

838051

Other (OTH)

AF:

0.153

AC:

6986

AN:

45770

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

5906

11812

17717

23623

29529

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.144

AC:

15917

AN:

110909

Hom.:

858

Cov.:

AF XY:

0.141

AC XY:

4678

AN XY:

33189

show subpopulations

African (AFR)

AF:

0.115

AC:

3524

AN:

30521

American (AMR)

AF:

0.108

AC:

1130

AN:

10485

Ashkenazi Jewish (ASJ)

AF:

0.146

AC:

384

AN:

2637

East Asian (EAS)

AF:

0.127

AC:

442

AN:

3472

South Asian (SAS)

AF:

0.191

AC:

499

AN:

2609

European-Finnish (FIN)

AF:

0.165

AC:

981

AN:

5954

Middle Eastern (MID)

AF:

0.0926

AC:

AN:

216

European-Non Finnish (NFE)

AF:

0.164

AC:

8647

AN:

52842

Other (OTH)

AF:

0.118

AC:

177

AN:

1502

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

485

969

1454

1938

2423

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.150

Hom.:

1254

Bravo

AF:

0.137

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.70

(source)

DANN

Benign

0.49

PhyloP100

0.29

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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chrX-141908578-G-A

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