Variant X-141906122-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_005462.5(MAGEC1):c.718T>G(p.Ser240Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000234 in 787,751 control chromosomes in the GnomAD database, including 8 homozygotes. There are 57 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. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00071 ( 1 hom., 14 hem., cov: 20)

Exomes 𝑓: 0.00017 ( 7 hom. 43 hem. )

Consequence

MAGEC1
NM_005462.5 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.196

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0056882203).

BP6

Variant X-141906122-T-G is Benign according to our data. Variant chrX-141906122-T-G is described in ClinVar as [Benign]. Clinvar id is 2661558.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAd4 at 14 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAGEC1	NM_005462.5 linkuse as main transcript	c.718T>G	p.Ser240Ala	missense_variant	4/4	ENST00000285879.5
MAGEC1	XM_011531418.3 linkuse as main transcript	c.718T>G	p.Ser240Ala	missense_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAGEC1	ENST00000285879.5 linkuse as main transcript	c.718T>G	p.Ser240Ala	missense_variant	4/4	1	NM_005462.5	P3	O60732-1
MAGEC1	ENST00000406005.2 linkuse as main transcript	c.-115+575T>G		intron_variant		1		A2	O60732-2

Frequencies

GnomAD3 genomes

AF:

0.000707

AC:

AN:

96216

Hom.:

Cov.:

AF XY:

0.000559

AC XY:

AN XY:

25046

show subpopulations

Gnomad AFR

AF:

0.00239

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000328

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000510

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000216

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000132

AC:

AN:

174270

Hom.:

AF XY:

0.000260

AC XY:

AN XY:

61508

show subpopulations

Gnomad AFR exome

AF:

0.00140

Gnomad AMR exome

AF:

0.000113

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000580

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000256

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000168

AC:

116

AN:

691498

Hom.:

Cov.:

AF XY:

0.000213

AC XY:

AN XY:

201474

show subpopulations

Gnomad4 AFR exome

AF:

0.00480

Gnomad4 AMR exome

AF:

0.000254

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000810

Gnomad4 OTH exome

AF:

0.000217

GnomAD4 genome

AF:

0.000706

AC:

AN:

96253

Hom.:

Cov.:

AF XY:

0.000558

AC XY:

AN XY:

25095

show subpopulations

Gnomad4 AFR

AF:

0.00238

Gnomad4 AMR

AF:

0.000327

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000512

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000216

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000931

Hom.:

ESP6500AA

AF:

0.0126

AC:

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.00134

AC:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2022

MAGEC1: BP4, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.76

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.36

DANN

Benign

0.23

DEOGEN2

Benign

0.0056

FATHMM_MKL

Benign

0.027

LIST_S2

Benign

0.13

MetaRNN

Benign

0.0057

MetaSVM

Benign

-0.94

MutationAssessor

Benign

1.5

MutationTaster

Benign

0.95

D;N

PrimateAI

Benign

0.45

PROVEAN

Benign

-0.17

REVEL

Benign

0.016

Sift

Benign

0.041

Sift4G

Uncertain

0.010

Polyphen

0.41

Vest4

0.086

MVP

0.061

ClinPred

0.0078

Varity_R

0.091

gMVP

0.0091

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over