Variant chrX-141906805-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000285879.5(MAGEC1):c.1401C>G(p.His467Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 1,194,297 control chromosomes in the GnomAD database, including 24,980 homozygotes. There are 88,851 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.21 ( 1882 hom., 5096 hem., cov: 21)

Exomes 𝑓: 0.24 ( 23098 hom. 83755 hem. )

Consequence

MAGEC1
ENST00000285879.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.303

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005238831).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 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.1401C>G	p.His467Gln	missense_variant	4/4	ENST00000285879.5	NP_005453.2	O60732-1
MAGEC1	XM_011531418.3 linkuse as main transcript	c.1401C>G	p.His467Gln	missense_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.1401C>G	p.His467Gln	missense_variant	4/4	1	NM_005462.5	ENSP00000285879.4		O60732-1
MAGEC1	ENST00000406005.2 linkuse as main transcript	c.-115+1258C>G		intron_variant		1		ENSP00000385500.2		O60732-2

Frequencies

GnomAD3 genomes

AF:

0.213

AC:

21598

AN:

101248

Hom.:

1883

Cov.:

AF XY:

0.188

AC XY:

5098

AN XY:

27070

show subpopulations

Gnomad AFR

AF:

0.190

Gnomad AMI

AF:

0.311

Gnomad AMR

AF:

0.157

Gnomad ASJ

AF:

0.253

Gnomad EAS

AF:

0.00362

Gnomad SAS

AF:

0.0633

Gnomad FIN

AF:

0.178

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.257

Gnomad OTH

AF:

0.193

GnomAD3 exomes

AF:

0.182

AC:

33137

AN:

181674

Hom.:

2421

AF XY:

0.183

AC XY:

12285

AN XY:

67206

show subpopulations

Gnomad AFR exome

AF:

0.182

Gnomad AMR exome

AF:

0.0991

Gnomad ASJ exome

AF:

0.253

Gnomad EAS exome

AF:

0.00355

Gnomad SAS exome

AF:

0.0680

Gnomad FIN exome

AF:

0.197

Gnomad NFE exome

AF:

0.257

Gnomad OTH exome

AF:

0.204

GnomAD4 exome

AF:

0.239

AC:

260956

AN:

1092999

Hom.:

23098

Cov.:

AF XY:

0.232

AC XY:

83755

AN XY:

360471

show subpopulations

Gnomad4 AFR exome

AF:

0.178

Gnomad4 AMR exome

AF:

0.106

Gnomad4 ASJ exome

AF:

0.254

Gnomad4 EAS exome

AF:

0.00173

Gnomad4 SAS exome

AF:

0.0741

Gnomad4 FIN exome

AF:

0.199

Gnomad4 NFE exome

AF:

0.268

Gnomad4 OTH exome

AF:

0.225

GnomAD4 genome

AF:

0.213

AC:

21587

AN:

101298

Hom.:

1882

Cov.:

AF XY:

0.188

AC XY:

5096

AN XY:

27120

show subpopulations

Gnomad4 AFR

AF:

0.190

Gnomad4 AMR

AF:

0.156

Gnomad4 ASJ

AF:

0.253

Gnomad4 EAS

AF:

0.00363

Gnomad4 SAS

AF:

0.0618

Gnomad4 FIN

AF:

0.178

Gnomad4 NFE

AF:

0.257

Gnomad4 OTH

AF:

0.190

Alfa

AF:

0.146

Hom.:

997

Bravo

AF:

0.207

TwinsUK

AF:

0.261

AC:

967

ALSPAC

AF:

0.256

AC:

740

ESP6500AA

AF:

0.195

AC:

749

ESP6500EA

AF:

0.253

AC:

1702

ExAC

AF:

0.188

AC:

22770

EpiCase

AF:

0.258

EpiControl

AF:

0.253

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-1.1

BayesDel_noAF

Benign

-1.2

CADD

Benign

0.0030

DANN

Benign

0.25

DEOGEN2

Benign

0.0013

FATHMM_MKL

Benign

0.0019

LIST_S2

Benign

0.16

MetaRNN

Benign

0.0052

MetaSVM

Benign

-0.91

MutationAssessor

Benign

-0.90

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.39

PROVEAN

Benign

0.16

REVEL

Benign

0.071

Sift

Benign

0.47

Sift4G

Benign

0.11

Polyphen

0.0010

Vest4

0.013

MutPred

0.14

Gain of solvent accessibility (P = 0.0837);

ClinPred

0.00087

Varity_R

0.082

gMVP

0.0094

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