Variant X-142203164-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_016249.4(MAGEC2):c.824C>G(p.Thr275Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00899 in 1,209,412 control chromosomes in the GnomAD database, including 60 homozygotes. There are 3,561 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0081 ( 5 hom., 336 hem., cov: 22)

Exomes 𝑓: 0.0091 ( 55 hom. 3225 hem. )

Consequence

MAGEC2
NM_016249.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.853

Variant links:

Genes affected

MAGEC2 (HGNC:13574): (MAGE family member C2) This gene is a member of the MAGEC gene family. It is not expressed in normal tissues, except for testis, and is expressed in tumors of various histological types. This gene and the other MAGEC genes are clustered on chromosome Xq26-q27. [provided by RefSeq, Oct 2009]

MAGEC2 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0038247705).

BP6

Variant X-142203164-G-C is Benign according to our data. Variant chrX-142203164-G-C is described in ClinVar as [Benign]. Clinvar id is 784434.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGEC2	NM_016249.4 linkuse as main transcript	c.824C>G	p.Thr275Ser	missense_variant	3/3	ENST00000247452.4	NP_057333.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAGEC2	ENST00000247452.4 linkuse as main transcript	c.824C>G	p.Thr275Ser	missense_variant	3/3	1	NM_016249.4	ENSP00000354660	P1
	ENST00000664519.1 linkuse as main transcript	n.300+7380G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.00812

AC:

904

AN:

111338

Hom.:

Cov.:

AF XY:

0.0100

AC XY:

336

AN XY:

33526

show subpopulations

Gnomad AFR

AF:

0.000556

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000759

Gnomad ASJ

AF:

0.0185

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0562

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00919

Gnomad OTH

AF:

0.00401

GnomAD3 exomes

AF:

0.0100

AC:

1836

AN:

182804

Hom.:

AF XY:

0.00955

AC XY:

644

AN XY:

67462

show subpopulations

Gnomad AFR exome

AF:

0.000612

Gnomad AMR exome

AF:

0.000255

Gnomad ASJ exome

AF:

0.0183

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0547

Gnomad NFE exome

AF:

0.00952

Gnomad OTH exome

AF:

0.00799

GnomAD4 exome

AF:

0.00908

AC:

9970

AN:

1098019

Hom.:

Cov.:

AF XY:

0.00887

AC XY:

3225

AN XY:

363391

show subpopulations

Gnomad4 AFR exome

AF:

0.000720

Gnomad4 AMR exome

AF:

0.000511

Gnomad4 ASJ exome

AF:

0.0182

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000185

Gnomad4 FIN exome

AF:

0.0514

Gnomad4 NFE exome

AF:

0.00849

Gnomad4 OTH exome

AF:

0.00757

GnomAD4 genome

AF:

0.00812

AC:

904

AN:

111393

Hom.:

Cov.:

AF XY:

0.0100

AC XY:

336

AN XY:

33591

show subpopulations

Gnomad4 AFR

AF:

0.000554

Gnomad4 AMR

AF:

0.000758

Gnomad4 ASJ

AF:

0.0185

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.0562

Gnomad4 NFE

AF:

0.00919

Gnomad4 OTH

AF:

0.00396

Alfa

AF:

0.0102

Hom.:

Bravo

AF:

0.00443

TwinsUK

AF:

0.00890

AC:

ALSPAC

AF:

0.00935

AC:

ESP6500AA

AF:

0.00130

AC:

ESP6500EA

AF:

0.00788

AC:

ExAC

AF:

0.00925

AC:

1123

EpiCase

AF:

0.00845

EpiControl

AF:

0.00640

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Mar 02, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.28

BayesDel_addAF

Benign

-0.61

BayesDel_noAF

Benign

-0.64

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.23

FATHMM_MKL

Benign

0.049

LIST_S2

Benign

0.62

MetaRNN

Benign

0.0038

MetaSVM

Benign

-1.1

MutationAssessor

Pathogenic

3.0

MutationTaster

Benign

1.0

PrimateAI

Benign

0.40

PROVEAN

Uncertain

-4.0

REVEL

Benign

0.080

Sift

Pathogenic

0.0

Sift4G

Pathogenic

0.0

Polyphen

0.99

Vest4

0.22

MutPred

0.89

Loss of ubiquitination at K276 (P = 0.0699);

MPC

0.018

ClinPred

0.078

GERP RS

0.99

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.75

gMVP

0.42

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