Variant rs12845617 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

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. Variant has been reported in Lovd as Likely benign (no stars).

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

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 made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

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

BP6

Variant X-141908578-G-A is Benign according to our data. Variant chrX-141908578-G-A is described in Lovd as [Likely_benign].

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/exons	MANE	Protein	UniProt
MAGEC1	NM_005462.5 linkuse as main transcript	c.3174G>A	p.Glu1058Glu	synonymous_variant	4/4	ENST00000285879.5	NP_005453.2	O60732-1
MAGEC1	XM_011531418.3 linkuse as main transcript	c.3174G>A	p.Glu1058Glu	synonymous_variant	4/4		XP_011529720.1	O60732-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAGEC1	ENST00000285879.5 linkuse as main transcript	c.3174G>A	p.Glu1058Glu	synonymous_variant	4/4	1	NM_005462.5	ENSP00000285879.4		O60732-1
MAGEC1	ENST00000406005.2 linkuse as main transcript	c.375G>A	p.Glu125Glu	synonymous_variant	4/4	1		ENSP00000385500.2		O60732-2

Frequencies

GnomAD3 genomes

AF:

0.144

AC:

15917

AN:

110857

Hom.:

860

Cov.:

AF XY:

0.141

AC XY:

4676

AN XY:

33127

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

GnomAD3 exomes

AF:

0.148

AC:

25829

AN:

174142

Hom.:

1287

AF XY:

0.153

AC XY:

9153

AN XY:

59686

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 SAS exome

AF:

0.198

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

Gnomad4 AFR exome

AF:

0.119

Gnomad4 AMR exome

AF:

0.0880

Gnomad4 ASJ exome

AF:

0.146

Gnomad4 EAS exome

AF:

0.129

Gnomad4 SAS exome

AF:

0.195

Gnomad4 FIN exome

AF:

0.177

Gnomad4 NFE exome

AF:

0.160

Gnomad4 OTH exome

AF:

0.153

GnomAD4 genome

AF:

0.144

AC:

15917

AN:

110909

Hom.:

858

Cov.:

AF XY:

0.141

AC XY:

4678

AN XY:

33189

show subpopulations

Gnomad4 AFR

AF:

0.115

Gnomad4 AMR

AF:

0.108

Gnomad4 ASJ

AF:

0.146

Gnomad4 EAS

AF:

0.127

Gnomad4 SAS

AF:

0.191

Gnomad4 FIN

AF:

0.165

Gnomad4 NFE

AF:

0.164

Gnomad4 OTH

AF:

0.118

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

DANN

Benign

0.49

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

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