dbSNP rs41300301: MAGEC1:c.*53C>T (chrX-141908886-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005462.5(MAGEC1):c.*53C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 1,061,261 control chromosomes in the GnomAD database, including 3,900 homozygotes. There are 32,708 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 0.086 ( 323 hom., 2703 hem., cov: 23)

Exomes 𝑓: 0.10 ( 3577 hom. 30005 hem. )

Consequence

MAGEC1
NM_005462.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.92

Publications

4 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAGEC1	NM_005462.5 link	c.*53C>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000285879.5	NP_005453.2	O60732-1
MAGEC1	XM_011531418.3 link	c.*53C>T		3_prime_UTR_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.*53C>T		3_prime_UTR_variant	Exon 4 of 4	1	NM_005462.5	ENSP00000285879.4		O60732-1
MAGEC1	ENST00000406005.2 link	c.*53C>T		3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000385500.2		O60732-2

Frequencies

GnomAD3 genomes

AF:

0.0857

AC:

9533

AN:

111293

Hom.:

325

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0695

Gnomad AMI

AF:

0.0278

Gnomad AMR

AF:

0.0672

Gnomad ASJ

AF:

0.0348

Gnomad EAS

AF:

0.0482

Gnomad SAS

AF:

0.133

Gnomad FIN

AF:

0.0888

Gnomad MID

AF:

0.0549

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.0855

GnomAD4 exome

AF:

0.104

AC:

98918

AN:

949917

Hom.:

3577

Cov.:

AF XY:

0.114

AC XY:

30005

AN XY:

263001

show subpopulations

African (AFR)

AF:

0.0787

AC:

1776

AN:

22575

American (AMR)

AF:

0.0872

AC:

2151

AN:

24663

Ashkenazi Jewish (ASJ)

AF:

0.0394

AC:

572

AN:

14527

East Asian (EAS)

AF:

0.0473

AC:

1388

AN:

29335

South Asian (SAS)

AF:

0.141

AC:

5662

AN:

40242

European-Finnish (FIN)

AF:

0.0921

AC:

3365

AN:

36518

Middle Eastern (MID)

AF:

0.109

AC:

394

AN:

3628

European-Non Finnish (NFE)

AF:

0.108

AC:

79841

AN:

737899

Other (OTH)

AF:

0.0930

AC:

3769

AN:

40530

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

3139

6278

9416

12555

15694

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3112

6224

9336

12448

15560

<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:

0.0856

AC:

9531

AN:

111344

Hom.:

323

Cov.:

AF XY:

0.0805

AC XY:

2703

AN XY:

33566

show subpopulations

African (AFR)

AF:

0.0696

AC:

2134

AN:

30678

American (AMR)

AF:

0.0668

AC:

704

AN:

10535

Ashkenazi Jewish (ASJ)

AF:

0.0348

AC:

AN:

2641

East Asian (EAS)

AF:

0.0484

AC:

170

AN:

3515

South Asian (SAS)

AF:

0.131

AC:

342

AN:

2618

European-Finnish (FIN)

AF:

0.0888

AC:

528

AN:

5946

Middle Eastern (MID)

AF:

0.0556

AC:

AN:

216

European-Non Finnish (NFE)

AF:

0.102

AC:

5403

AN:

53008

Other (OTH)

AF:

0.0844

AC:

127

AN:

1504

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

318

636

955

1273

1591

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

228

342

456

570

<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:

0.0999

Hom.:

858

Bravo

AF:

0.0817

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.48

(source)

DANN

Benign

0.35

PhyloP100

-2.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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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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