Variant X-141906056-C-T 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.652C>T(p.Pro218Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000142 in 1,151,468 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 93 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00014 ( 0 hom., 4 hem., cov: 33)

Exomes 𝑓: 0.00014 ( 0 hom. 89 hem. )

Consequence

MAGEC1
NM_005462.5 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.140

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 -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.029827148).

BP6

Variant X-141906056-C-T is Benign according to our data. Variant chrX-141906056-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3024854.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGEC1	NM_005462.5 link	c.652C>T	p.Pro218Ser	missense_variant	4/4	ENST00000285879.5	NP_005453.2	O60732-1
MAGEC1	XM_011531418.3 link	c.652C>T	p.Pro218Ser	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 link	c.652C>T	p.Pro218Ser	missense_variant	4/4	1	NM_005462.5	ENSP00000285879.4		O60732-1
MAGEC1	ENST00000406005.2 link	c.-115+509C>T		intron_variant		1		ENSP00000385500.2		O60732-2

Frequencies

GnomAD3 genomes

AF:

0.000145

AC:

AN:

103668

Hom.:

Cov.:

AF XY:

0.000124

AC XY:

AN XY:

32286

show subpopulations

Gnomad AFR

AF:

0.000138

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000207

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000947

Gnomad SAS

AF:

0.00160

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000204

Gnomad OTH

AF:

0.000718

GnomAD4 exome

AF:

0.000141

AC:

148

AN:

1047761

Hom.:

Cov.:

105

AF XY:

0.000257

AC XY:

AN XY:

345851

show subpopulations

Gnomad4 AFR exome

AF:

0.000199

Gnomad4 AMR exome

AF:

0.000269

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00125

Gnomad4 SAS exome

AF:

0.000778

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000584

Gnomad4 OTH exome

AF:

0.000228

GnomAD4 genome

AF:

0.000145

AC:

AN:

103707

Hom.:

Cov.:

AF XY:

0.000124

AC XY:

AN XY:

32331

show subpopulations

Gnomad4 AFR

AF:

0.000138

Gnomad4 AMR

AF:

0.000207

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000950

Gnomad4 SAS

AF:

0.00160

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000204

Gnomad4 OTH

AF:

0.000707

ExAC

AF:

0.000304

AC:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2024

MAGEC1: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.20

BayesDel_addAF

Benign

-0.48

BayesDel_noAF

Benign

-0.92

CADD

Benign

8.0

DANN

Benign

0.25

DEOGEN2

Benign

0.0061

FATHMM_MKL

Benign

0.0073

LIST_S2

Benign

0.33

M_CAP

Benign

0.0037

MetaRNN

Benign

0.030

MetaSVM

Benign

-0.94

MutationAssessor

Benign

0.81

PrimateAI

Benign

0.44

PROVEAN

Benign

-1.1

REVEL

Benign

0.047

Sift

Pathogenic

0.0

Sift4G

Benign

0.22

Polyphen

0.0020

Vest4

0.050

MVP

0.048

ClinPred

0.22

Varity_R

0.074

gMVP

0.020

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